diff --git a/Rscript/Library/mzkit_app/man/mzkit/math/math/cosine.1 b/Rscript/Library/mzkit_app/man/mzkit/math/math/cosine.1 index bfa4c1dc40..d176499714 100644 --- a/Rscript/Library/mzkit_app/man/mzkit/math/math/cosine.1 +++ b/Rscript/Library/mzkit_app/man/mzkit/math/math/cosine.1 @@ -28,6 +28,50 @@ Do evaluate the spectra cosine similarity score .PP \fBenv\fB \fR\- -. .PP +.SH DETAILS +.PP +this function andalso produce the jaccard/entropy similarity of the spectrum inside the similarity result object +.PP +.SH EXAMPLES +.PP +# create the spectrum matrix object + # fragment data tagged with the source name title + let spec1 = libraryMatrix( + matrix = data.frame( + mz = c(169.071, 186.066, 186.0769), + intensity = c(7.917962, 1.021589, 100.0) + ), + title = "Demo MS1 Spectra", + centroid = TRUE + ); + let spec2 = libraryMatrix( + matrix = data.frame( + mz = c(120.212, 169.071, 186.066), + intensity = c(37.16, 66.83, 999.0) + ), + title = "Demo MS1 Spectra", + centroid = TRUE + ); + let compares = math::cosine(spec1, spec2); + let scores = as.data.frame(compares, scores_df = TRUE); + + print(scores); + # dimension scores + # ---------------------------------- + # + # [1, ] "forward cosine" 0.999925 + # [2, ] "reverse cosine" 0.999925 + # [3, ] "cosine" 0.999925 + # [4, ] "jaccard" 1 + # [5, ] "entropy" 0.999949 + # [6, ] "mirror" 1 + # [7, ] "mean" 0.99995 + # [8, ] "fragment hits" 2 + + svg(file = "figures/00_Mass_spectrometry/Math/03_compares.svg") { + plot(compares); + } +.PP .SH SEE ALSO math .SH FILES diff --git a/Rscript/Library/mzkit_app/src/mzDIA/mzDIA.vbproj b/Rscript/Library/mzkit_app/src/mzDIA/mzDIA.vbproj index a027412d31..e6827eed4a 100644 --- a/Rscript/Library/mzkit_app/src/mzDIA/mzDIA.vbproj +++ b/Rscript/Library/mzkit_app/src/mzDIA/mzDIA.vbproj @@ -158,6 +158,7 @@ + diff --git a/Rscript/Library/mzkit_app/src/mzkit/comprehensive/GCxGC.vb b/Rscript/Library/mzkit_app/src/mzkit/comprehensive/GCxGC.vb index d7b366272d..d5b4bce936 100644 --- a/Rscript/Library/mzkit_app/src/mzkit/comprehensive/GCxGC.vb +++ b/Rscript/Library/mzkit_app/src/mzkit/comprehensive/GCxGC.vb @@ -113,13 +113,13 @@ Module GCxGC ''' ''' - + Public Function TIC2D(TIC As ChromatogramTick(), modtime As Double) As Object Return TIC.Demodulate2D(modtime) End Function - Public Function TIC1D(matrix As D2Chromatogram()) As ChromatogramTick() + Public Function TIC1D(matrix As Chromatogram2DScan()) As ChromatogramTick() Return matrix _ .Select(Function(i) Return New ChromatogramTick With { @@ -181,7 +181,7 @@ Module GCxGC ''' this function will extract the TIC data by default. ''' - + Public Function create2DPeaks(raw As mzPack, Optional mz As Double = Double.NaN, Optional mzdiff As Object = "ppm:30", @@ -195,7 +195,7 @@ Module GCxGC End If Dim test As Tolerance = mzErr.TryCast(Of Tolerance) - Dim extract As Func(Of ScanMS1, D2Chromatogram) + Dim extract As Func(Of ScanMS1, Chromatogram2DScan) If extract_XIC Then extract = ExtractXIC(mz, mzdiff:=test) @@ -251,7 +251,7 @@ Module GCxGC ''' - Public Function saveCDF(TIC As D2Chromatogram(), file As Object, Optional env As Environment = Nothing) As Object + Public Function saveCDF(TIC As Chromatogram2DScan(), file As Object, Optional env As Environment = Nothing) As Object Dim filestream As [Variant](Of Stream, Message) = SMRUCC.Rsharp.GetFileStream(file, FileAccess.Write, env) If filestream Like GetType(Message) Then diff --git a/Rscript/Library/mzkit_app/src/mzkit/math/Math.vb b/Rscript/Library/mzkit_app/src/mzkit/math/Math.vb index 6da660ed71..9be170f22e 100644 --- a/Rscript/Library/mzkit_app/src/mzkit/math/Math.vb +++ b/Rscript/Library/mzkit_app/src/mzkit/math/Math.vb @@ -94,9 +94,9 @@ Imports SMRUCC.Rsharp.Runtime.Internal.Object Imports SMRUCC.Rsharp.Runtime.Interop Imports SMRUCC.Rsharp.Runtime.Vectorization Imports REnv = SMRUCC.Rsharp.Runtime +Imports RInternal = SMRUCC.Rsharp.Runtime.Internal Imports std = System.Math Imports stdVector = Microsoft.VisualBasic.Math.LinearAlgebra.Vector -Imports RInternal = SMRUCC.Rsharp.Runtime.Internal ''' ''' mass spectrometry data math toolkit @@ -206,19 +206,46 @@ Module MzMath ''' Private Function getAlignmentTable(align As AlignmentOutput, args As list, env As Environment) As dataframe - Dim mz As Double() = align.alignments.Select(Function(a) a.mz).ToArray - Dim query As Double() = align.alignments.Select(Function(a) a.query).ToArray - Dim reference As Double() = align.alignments.Select(Function(a) a.ref).ToArray - Dim da As String() = align.alignments.Select(Function(a) a.da).ToArray + Dim scores_df As Boolean = args.getValue("scores_df", env, [default]:=False) - Return New dataframe With { - .columns = New Dictionary(Of String, Array) From { - {"m/z", mz}, - {"query", query}, - {"ref", reference}, - {"da", da} + If scores_df Then + Dim df As New dataframe With { + .columns = New Dictionary(Of String, Array) } - } + + Call df.add("dimension", { + "forward cosine", "reverse cosine", + "cosine", + "jaccard", + "entropy", + "mirror", + "mean", + "fragment hits"}) + Call df.add("scores", { + align.forward, align.reverse, + align.cosine, + align.jaccard, + align.entropy, + align.mirror, + align.mean, + align.nhits}) + + Return df + Else + Dim mz As Double() = align.alignments.Select(Function(a) a.mz).ToArray + Dim query As Double() = align.alignments.Select(Function(a) a.query).ToArray + Dim reference As Double() = align.alignments.Select(Function(a) a.ref).ToArray + Dim da As String() = align.alignments.Select(Function(a) a.da).ToArray + + Return New dataframe With { + .columns = New Dictionary(Of String, Array) From { + {"m/z", mz}, + {"query", query}, + {"ref", reference}, + {"da", da} + } + } + End If End Function Private Function printCalculator(type As MzCalculator) As String @@ -620,6 +647,48 @@ Module MzMath ''' ''' ''' + ''' + ''' this function andalso produce the jaccard/entropy similarity of the spectrum inside the similarity result object + ''' + ''' + ''' # create the spectrum matrix object + ''' # fragment data tagged with the source name title + ''' let spec1 = libraryMatrix( + ''' matrix = data.frame( + ''' mz = c(169.071, 186.066, 186.0769), + ''' intensity = c(7.917962, 1.021589, 100.0) + ''' ), + ''' title = "Demo MS1 Spectra", + ''' centroid = TRUE + ''' ); + ''' let spec2 = libraryMatrix( + ''' matrix = data.frame( + ''' mz = c(120.212, 169.071, 186.066), + ''' intensity = c(37.16, 66.83, 999.0) + ''' ), + ''' title = "Demo MS1 Spectra", + ''' centroid = TRUE + ''' ); + ''' let compares = math::cosine(spec1, spec2); + ''' let scores = as.data.frame(compares, scores_df = TRUE); + ''' + ''' print(scores); + ''' # dimension scores + ''' # ---------------------------------- + ''' # <mode> <string> <double> + ''' # [1, ] "forward cosine" 0.999925 + ''' # [2, ] "reverse cosine" 0.999925 + ''' # [3, ] "cosine" 0.999925 + ''' # [4, ] "jaccard" 1 + ''' # [5, ] "entropy" 0.999949 + ''' # [6, ] "mirror" 1 + ''' # [7, ] "mean" 0.99995 + ''' # [8, ] "fragment hits" 2 + ''' + ''' svg(file = "figures/00_Mass_spectrometry/Math/03_compares.svg") { + ''' plot(compares); + ''' } + ''' Public Function cosine( query As Object, ref As Object, diff --git a/Rscript/Library/mzkit_app/src/mzkit/mzkit.vbproj b/Rscript/Library/mzkit_app/src/mzkit/mzkit.vbproj index f1ad3f1665..78364f7bf4 100644 --- a/Rscript/Library/mzkit_app/src/mzkit/mzkit.vbproj +++ b/Rscript/Library/mzkit_app/src/mzkit/mzkit.vbproj @@ -307,6 +307,7 @@ + diff --git a/Rscript/Library/mzkit_app/src/mzplot/Visual.vb b/Rscript/Library/mzkit_app/src/mzplot/Visual.vb index b66fd0a952..f89c9b5ea4 100644 --- a/Rscript/Library/mzkit_app/src/mzplot/Visual.vb +++ b/Rscript/Library/mzkit_app/src/mzplot/Visual.vb @@ -1,62 +1,62 @@ #Region "Microsoft.VisualBasic::69b45a2a18279e690fc3c632240a18de, Rscript\Library\mzkit_app\src\mzplot\Visual.vb" - ' Author: - ' - ' xieguigang (gg.xie@bionovogene.com, BioNovoGene Co., LTD.) - ' - ' Copyright (c) 2018 gg.xie@bionovogene.com, BioNovoGene Co., LTD. - ' - ' - ' MIT License - ' - ' - ' Permission is hereby granted, free of charge, to any person obtaining a copy - ' of this software and associated documentation files (the "Software"), to deal - ' in the Software without restriction, including without limitation the rights - ' to use, copy, modify, merge, publish, distribute, sublicense, and/or sell - ' copies of the Software, and to permit persons to whom the Software is - ' furnished to do so, subject to the following conditions: - ' - ' The above copyright notice and this permission notice shall be included in all - ' copies or substantial portions of the Software. - ' - ' THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR - ' IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, - ' FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE - ' AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER - ' LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, - ' OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE - ' SOFTWARE. - - - - ' /********************************************************************************/ - - ' Summaries: - - - ' Code Statistics: - - ' Total Lines: 891 - ' Code Lines: 699 (78.45%) - ' Comment Lines: 111 (12.46%) - ' - Xml Docs: 91.89% - ' - ' Blank Lines: 81 (9.09%) - ' File Size: 40.74 KB - - - ' Module Visual - ' - ' Function: assembleOverlaps, ParseSpectrumAlignment, plotAlignments, plotChromatogram, PlotGCxGCHeatMap - ' plotGCxGCTic2D, plotMolecularNetworkingHistogram, plotMS, plotOverlaps, plotPeaktable - ' plotRawChromatogram, PlotRawScatter, plotRtShifts, plotSignal, plotSignal2 - ' plotTIC, plotTIC2, PlotUVSignals, Snapshot3D, SpectrumPlot - ' XicScatterDensity - ' - ' Sub: Main - ' - ' /********************************************************************************/ +' Author: +' +' xieguigang (gg.xie@bionovogene.com, BioNovoGene Co., LTD.) +' +' Copyright (c) 2018 gg.xie@bionovogene.com, BioNovoGene Co., LTD. +' +' +' MIT License +' +' +' Permission is hereby granted, free of charge, to any person obtaining a copy +' of this software and associated documentation files (the "Software"), to deal +' in the Software without restriction, including without limitation the rights +' to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +' copies of the Software, and to permit persons to whom the Software is +' furnished to do so, subject to the following conditions: +' +' The above copyright notice and this permission notice shall be included in all +' copies or substantial portions of the Software. +' +' THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +' IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +' FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +' AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +' LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +' OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +' SOFTWARE. + + + +' /********************************************************************************/ + +' Summaries: + + +' Code Statistics: + +' Total Lines: 891 +' Code Lines: 699 (78.45%) +' Comment Lines: 111 (12.46%) +' - Xml Docs: 91.89% +' +' Blank Lines: 81 (9.09%) +' File Size: 40.74 KB + + +' Module Visual +' +' Function: assembleOverlaps, ParseSpectrumAlignment, plotAlignments, plotChromatogram, PlotGCxGCHeatMap +' plotGCxGCTic2D, plotMolecularNetworkingHistogram, plotMS, plotOverlaps, plotPeaktable +' plotRawChromatogram, PlotRawScatter, plotRtShifts, plotSignal, plotSignal2 +' plotTIC, plotTIC2, PlotUVSignals, Snapshot3D, SpectrumPlot +' XicScatterDensity +' +' Sub: Main +' +' /********************************************************************************/ #End Region @@ -105,6 +105,8 @@ Imports SMRUCC.Rsharp.Runtime.Vectorization Imports Chromatogram = BioNovoGene.Analytical.MassSpectrometry.Math.Chromatogram.Chromatogram Imports RInternal = SMRUCC.Rsharp.Runtime.Internal Imports BioNovoGene.Analytical.MassSpectrometry.Math.MRM.Data +Imports BioNovoGene.Analytical.MassSpectrometry.GCxGC + #If NET48 Then @@ -305,7 +307,7 @@ Module Visual End Function - Private Function plotGCxGCTic2D(x As D2Chromatogram(), args As list, env As Environment) As Object + Private Function plotGCxGCTic2D(x As Chromatogram2DScan(), args As list, env As Environment) As Object Dim theme As New Theme With { .padding = args.getValue("padding", env, "padding: 250px 500px 200px 200px;"), .colorSet = args.getValue("colorSet", env, "Jet") @@ -448,7 +450,7 @@ Module Visual - Private Function plotTIC2(x As D2Chromatogram, args As list, env As Environment) As Object + Private Function plotTIC2(x As Chromatogram2DScan, args As list, env As Environment) As Object Return x.chromatogram.plotTIC(args, env) End Function @@ -570,9 +572,9 @@ Module Visual Dim rt_size = InteropArgumentHelper.getSize(rt_width, env, "5,0.5").Split(","c).Select(AddressOf Val).ToArray Dim samples = GCxGC.getNames _ .Select(Function(name) - Return New NamedCollection(Of D2Chromatogram) With { + Return New NamedCollection(Of Chromatogram2DScan) With { .name = name, - .value = GCxGC.getValue(Of D2Chromatogram())(name, env, Nothing) + .value = GCxGC.getValue(Of Chromatogram2DScan())(name, env, Nothing) } End Function) _ .Where(Function(d) Not d.value.IsNullOrEmpty) _ @@ -955,11 +957,35 @@ Module Visual ''' ''' - Public Function XicScatterDensity( ms1 As Object, Optional env As Environment = Nothing) As Object + Public Function XicScatterDensity( ms1 As Object, + Optional mz As Double? = Nothing, + Optional mass_err As Object = "ppm:20", + + Optional args As list = Nothing, + Optional env As Environment = Nothing) As Object + Dim pull As pipeline = pipeline.TryCreatePipeline(Of ms1_scan)(ms1, env) If pull.isError Then + Return pull.getError + End If + + Dim scatter = pull.populates(Of ms1_scan)(env).ToArray + Dim mass_win = Math.getTolerance(mass_err, env) + If mass_win Like GetType(Message) Then + Return mass_win.TryCast(Of Message) End If + + If mz Is Nothing Then + mz = scatter.Select(Function(a) a.mz).Average + End If + + Dim theme As New Theme + Dim app As New PlotMassWindowXIC(scatter, CDbl(mz), mass_win.TryCast(Of Tolerance), theme) + Dim dpi As Integer = graphicsPipeline.getDpi(args.slots, env, [default]:=100) + Dim size As SizeF = graphicsPipeline.getSize(args, env, New SizeF(3600, 2700)) + + Return app.Plot($"{size.Width},{size.Height}", dpi, env.getDriver) End Function End Module diff --git a/Rscript/Library/mzkit_app/vignettes/R/docs/.extract_pubmed_evidence.html b/Rscript/Library/mzkit_app/vignettes/R/docs/.extract_pubmed_evidence.html index c6e5412331..0079dc8445 100644 --- a/Rscript/Library/mzkit_app/vignettes/R/docs/.extract_pubmed_evidence.html +++ b/Rscript/Library/mzkit_app/vignettes/R/docs/.extract_pubmed_evidence.html @@ -5,7 +5,7 @@ .extract_pubmed_evidence - + @@ -61,8 +61,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/R/docs/.graph_table.html b/Rscript/Library/mzkit_app/vignettes/R/docs/.graph_table.html index e007de03c1..3f8aff6288 100644 --- a/Rscript/Library/mzkit_app/vignettes/R/docs/.graph_table.html +++ b/Rscript/Library/mzkit_app/vignettes/R/docs/.graph_table.html @@ -5,7 +5,7 @@ .graph_table - + @@ -61,8 +61,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/R/docs/.onLoad.html b/Rscript/Library/mzkit_app/vignettes/R/docs/.onLoad.html index 9afa07c444..5cc290149c 100644 --- a/Rscript/Library/mzkit_app/vignettes/R/docs/.onLoad.html +++ b/Rscript/Library/mzkit_app/vignettes/R/docs/.onLoad.html @@ -5,7 +5,7 @@ Hello, world! This is an example function named 'hello' which prints 'Hello, world!'. You can learn more about package authoring with RStudio at: http://r-pkgs.had.co.nz/ Some useful keyboard shortcuts for package authoring: Install Package: 'Ctrl + Shift + B' Check Package: 'Ctrl + Shift + E' Test Package: 'Ctrl + Shift + T' - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/R/docs/.term_maps.html b/Rscript/Library/mzkit_app/vignettes/R/docs/.term_maps.html index 21cc6c7602..ce1ccbd6c8 100644 --- a/Rscript/Library/mzkit_app/vignettes/R/docs/.term_maps.html +++ b/Rscript/Library/mzkit_app/vignettes/R/docs/.term_maps.html @@ -5,7 +5,7 @@ .term_maps - + @@ -61,8 +61,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/R/docs/ANOVAGroup.html b/Rscript/Library/mzkit_app/vignettes/R/docs/ANOVAGroup.html index aa63bcb09e..2be3a8b352 100644 --- a/Rscript/Library/mzkit_app/vignettes/R/docs/ANOVAGroup.html +++ b/Rscript/Library/mzkit_app/vignettes/R/docs/ANOVAGroup.html @@ -5,7 +5,7 @@ Create a dataset for evaluate ANOVA p-value - + @@ -67,8 +67,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/R/docs/GCMS_contentTable.html b/Rscript/Library/mzkit_app/vignettes/R/docs/GCMS_contentTable.html index 551894cfec..ae7325b0c1 100644 --- a/Rscript/Library/mzkit_app/vignettes/R/docs/GCMS_contentTable.html +++ b/Rscript/Library/mzkit_app/vignettes/R/docs/GCMS_contentTable.html @@ -5,7 +5,7 @@ Create content levels table - + @@ -63,8 +63,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/R/docs/GCMS_linearReport.html b/Rscript/Library/mzkit_app/vignettes/R/docs/GCMS_linearReport.html index 24ddac86ed..ba844a6a2f 100644 --- a/Rscript/Library/mzkit_app/vignettes/R/docs/GCMS_linearReport.html +++ b/Rscript/Library/mzkit_app/vignettes/R/docs/GCMS_linearReport.html @@ -5,7 +5,7 @@ GCMS_linearReport - + @@ -61,8 +61,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/R/docs/GCMS_linears.html b/Rscript/Library/mzkit_app/vignettes/R/docs/GCMS_linears.html index 6171b79f37..5c7f2f9a1d 100644 --- a/Rscript/Library/mzkit_app/vignettes/R/docs/GCMS_linears.html +++ b/Rscript/Library/mzkit_app/vignettes/R/docs/GCMS_linears.html @@ -5,7 +5,7 @@ Create reference linears for GCMS sim data - + @@ -78,8 +78,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/R/docs/GCMS_quantify.html b/Rscript/Library/mzkit_app/vignettes/R/docs/GCMS_quantify.html index c04309604a..617487edcf 100644 --- a/Rscript/Library/mzkit_app/vignettes/R/docs/GCMS_quantify.html +++ b/Rscript/Library/mzkit_app/vignettes/R/docs/GCMS_quantify.html @@ -5,7 +5,7 @@ GCMS_quantify - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/R/docs/__deconv_gcms_single.html b/Rscript/Library/mzkit_app/vignettes/R/docs/__deconv_gcms_single.html index 92373e5074..c0bab4b2a6 100644 --- a/Rscript/Library/mzkit_app/vignettes/R/docs/__deconv_gcms_single.html +++ b/Rscript/Library/mzkit_app/vignettes/R/docs/__deconv_gcms_single.html @@ -5,7 +5,7 @@ __deconv_gcms_single - + @@ -61,8 +61,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/R/docs/__ms1_xic_bins_single.html b/Rscript/Library/mzkit_app/vignettes/R/docs/__ms1_xic_bins_single.html index c826e4010e..290cdbc13a 100644 --- a/Rscript/Library/mzkit_app/vignettes/R/docs/__ms1_xic_bins_single.html +++ b/Rscript/Library/mzkit_app/vignettes/R/docs/__ms1_xic_bins_single.html @@ -5,7 +5,7 @@ export XIC data for a single rawdata file - + @@ -71,8 +71,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/R/docs/convertToMzPack.html b/Rscript/Library/mzkit_app/vignettes/R/docs/convertToMzPack.html index c378a96e00..cdda6eff99 100644 --- a/Rscript/Library/mzkit_app/vignettes/R/docs/convertToMzPack.html +++ b/Rscript/Library/mzkit_app/vignettes/R/docs/convertToMzPack.html @@ -5,7 +5,7 @@ Convert to mzpack data object - + @@ -63,8 +63,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/R/docs/deconv_gcms.html b/Rscript/Library/mzkit_app/vignettes/R/docs/deconv_gcms.html index 9524fd4ddf..61fc077dd5 100644 --- a/Rscript/Library/mzkit_app/vignettes/R/docs/deconv_gcms.html +++ b/Rscript/Library/mzkit_app/vignettes/R/docs/deconv_gcms.html @@ -5,7 +5,7 @@ Make expression peak table deconvolution of the GCMS rawdata - + @@ -63,8 +63,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/R/docs/getDataValues.html b/Rscript/Library/mzkit_app/vignettes/R/docs/getDataValues.html index 3044c226a7..7bad9dde12 100644 --- a/Rscript/Library/mzkit_app/vignettes/R/docs/getDataValues.html +++ b/Rscript/Library/mzkit_app/vignettes/R/docs/getDataValues.html @@ -5,7 +5,7 @@ get values in section$data - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/R/docs/getQuery.html b/Rscript/Library/mzkit_app/vignettes/R/docs/getQuery.html index fb5d7d9fd6..007f334902 100644 --- a/Rscript/Library/mzkit_app/vignettes/R/docs/getQuery.html +++ b/Rscript/Library/mzkit_app/vignettes/R/docs/getQuery.html @@ -5,7 +5,7 @@ getQuery - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/R/docs/get_representives.html b/Rscript/Library/mzkit_app/vignettes/R/docs/get_representives.html index 6492c12b44..202db48153 100644 --- a/Rscript/Library/mzkit_app/vignettes/R/docs/get_representives.html +++ b/Rscript/Library/mzkit_app/vignettes/R/docs/get_representives.html @@ -5,7 +5,7 @@ Get n representive spectrums via molecular networking - + @@ -83,8 +83,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/R/docs/ionPairsFromMsl.html b/Rscript/Library/mzkit_app/vignettes/R/docs/ionPairsFromMsl.html index ab33d173a2..d371ae645d 100644 --- a/Rscript/Library/mzkit_app/vignettes/R/docs/ionPairsFromMsl.html +++ b/Rscript/Library/mzkit_app/vignettes/R/docs/ionPairsFromMsl.html @@ -5,7 +5,7 @@ Read ion pairs data from MSL dataset - + @@ -68,8 +68,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/R/docs/kegg_compounds.html b/Rscript/Library/mzkit_app/vignettes/R/docs/kegg_compounds.html index f600f6344c..16466980bc 100644 --- a/Rscript/Library/mzkit_app/vignettes/R/docs/kegg_compounds.html +++ b/Rscript/Library/mzkit_app/vignettes/R/docs/kegg_compounds.html @@ -5,7 +5,7 @@ Load the kegg database for the annotation - + @@ -79,8 +79,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/R/docs/knowledge_graph.html b/Rscript/Library/mzkit_app/vignettes/R/docs/knowledge_graph.html index 2b9e065a4b..c26c34d48e 100644 --- a/Rscript/Library/mzkit_app/vignettes/R/docs/knowledge_graph.html +++ b/Rscript/Library/mzkit_app/vignettes/R/docs/knowledge_graph.html @@ -5,7 +5,7 @@ Query pubchem for knowledge network - + @@ -64,8 +64,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/R/docs/lipidmaps_repo.html b/Rscript/Library/mzkit_app/vignettes/R/docs/lipidmaps_repo.html index a44fdee2ba..0a647c94e8 100644 --- a/Rscript/Library/mzkit_app/vignettes/R/docs/lipidmaps_repo.html +++ b/Rscript/Library/mzkit_app/vignettes/R/docs/lipidmaps_repo.html @@ -5,7 +5,7 @@ Load lipidmaps data repository from internal data pack - + @@ -70,8 +70,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/R/docs/loadTree.html b/Rscript/Library/mzkit_app/vignettes/R/docs/loadTree.html index f86ced8d90..fa951f2be6 100644 --- a/Rscript/Library/mzkit_app/vignettes/R/docs/loadTree.html +++ b/Rscript/Library/mzkit_app/vignettes/R/docs/loadTree.html @@ -5,7 +5,7 @@ Load spectrum tree from raw data files - + @@ -63,8 +63,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/R/docs/load_LMSD.html b/Rscript/Library/mzkit_app/vignettes/R/docs/load_LMSD.html index 2301cf4404..8bfa370875 100644 --- a/Rscript/Library/mzkit_app/vignettes/R/docs/load_LMSD.html +++ b/Rscript/Library/mzkit_app/vignettes/R/docs/load_LMSD.html @@ -5,7 +5,7 @@ load the lipidmaps raw database - + @@ -64,8 +64,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/R/docs/mesh_model.html b/Rscript/Library/mzkit_app/vignettes/R/docs/mesh_model.html index 31306c00f8..1773187cf8 100644 --- a/Rscript/Library/mzkit_app/vignettes/R/docs/mesh_model.html +++ b/Rscript/Library/mzkit_app/vignettes/R/docs/mesh_model.html @@ -5,7 +5,7 @@ Load mesh background model from run enrichment analysis - + @@ -61,8 +61,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/R/docs/ms1_mz_bins.html b/Rscript/Library/mzkit_app/vignettes/R/docs/ms1_mz_bins.html index 653c8129d5..24e07babf7 100644 --- a/Rscript/Library/mzkit_app/vignettes/R/docs/ms1_mz_bins.html +++ b/Rscript/Library/mzkit_app/vignettes/R/docs/ms1_mz_bins.html @@ -5,7 +5,7 @@ Extract the ion m/z features - + @@ -64,8 +64,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/R/docs/ms1_peaktable.html b/Rscript/Library/mzkit_app/vignettes/R/docs/ms1_peaktable.html index b981ab31e7..5cbd44318b 100644 --- a/Rscript/Library/mzkit_app/vignettes/R/docs/ms1_peaktable.html +++ b/Rscript/Library/mzkit_app/vignettes/R/docs/ms1_peaktable.html @@ -5,7 +5,7 @@ Export peakstable data from the XIC rawdata files - + @@ -73,8 +73,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/R/docs/ms1_xic_bins.html b/Rscript/Library/mzkit_app/vignettes/R/docs/ms1_xic_bins.html index 5fc73a6b71..53ede10d1a 100644 --- a/Rscript/Library/mzkit_app/vignettes/R/docs/ms1_xic_bins.html +++ b/Rscript/Library/mzkit_app/vignettes/R/docs/ms1_xic_bins.html @@ -5,7 +5,7 @@ Create XIC rawdata file for run peaktable exports - + @@ -78,8 +78,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/R/docs/output_datatables.html b/Rscript/Library/mzkit_app/vignettes/R/docs/output_datatables.html index 608c116ab9..8eb6be7e3d 100644 --- a/Rscript/Library/mzkit_app/vignettes/R/docs/output_datatables.html +++ b/Rscript/Library/mzkit_app/vignettes/R/docs/output_datatables.html @@ -5,7 +5,7 @@ Output result data table - + @@ -61,8 +61,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/R/docs/pack_singleCells.html b/Rscript/Library/mzkit_app/vignettes/R/docs/pack_singleCells.html index 607290a4c1..a647254e24 100644 --- a/Rscript/Library/mzkit_app/vignettes/R/docs/pack_singleCells.html +++ b/Rscript/Library/mzkit_app/vignettes/R/docs/pack_singleCells.html @@ -5,7 +5,7 @@ pack the multiple single cells samples into one dataset. - + @@ -68,8 +68,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/R/docs/parseDescriptors.html b/Rscript/Library/mzkit_app/vignettes/R/docs/parseDescriptors.html index bbc84ef6f6..a4e3ddbae4 100644 --- a/Rscript/Library/mzkit_app/vignettes/R/docs/parseDescriptors.html +++ b/Rscript/Library/mzkit_app/vignettes/R/docs/parseDescriptors.html @@ -5,7 +5,7 @@ parseDescriptors - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/R/docs/parseNames.html b/Rscript/Library/mzkit_app/vignettes/R/docs/parseNames.html index 58d4b182c0..e493203c0c 100644 --- a/Rscript/Library/mzkit_app/vignettes/R/docs/parseNames.html +++ b/Rscript/Library/mzkit_app/vignettes/R/docs/parseNames.html @@ -5,7 +5,7 @@ parseNames - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/R/docs/parsePubchemMeta.html b/Rscript/Library/mzkit_app/vignettes/R/docs/parsePubchemMeta.html index 3d762dd241..972c793a9f 100644 --- a/Rscript/Library/mzkit_app/vignettes/R/docs/parsePubchemMeta.html +++ b/Rscript/Library/mzkit_app/vignettes/R/docs/parsePubchemMeta.html @@ -5,7 +5,7 @@ Parse the compound information - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/R/docs/parseXref.html b/Rscript/Library/mzkit_app/vignettes/R/docs/parseXref.html index a72109bed8..c880a194b9 100644 --- a/Rscript/Library/mzkit_app/vignettes/R/docs/parseXref.html +++ b/Rscript/Library/mzkit_app/vignettes/R/docs/parseXref.html @@ -5,7 +5,7 @@ parseXref - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/R/docs/plotLinears.html b/Rscript/Library/mzkit_app/vignettes/R/docs/plotLinears.html index d369f766f3..c24854b280 100644 --- a/Rscript/Library/mzkit_app/vignettes/R/docs/plotLinears.html +++ b/Rscript/Library/mzkit_app/vignettes/R/docs/plotLinears.html @@ -5,7 +5,7 @@ plotLinears - + @@ -62,8 +62,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/R/docs/preprocessing_expression.html b/Rscript/Library/mzkit_app/vignettes/R/docs/preprocessing_expression.html index 3d509ba000..b0e1e617b6 100644 --- a/Rscript/Library/mzkit_app/vignettes/R/docs/preprocessing_expression.html +++ b/Rscript/Library/mzkit_app/vignettes/R/docs/preprocessing_expression.html @@ -5,7 +5,7 @@ Normalize matrix sample data - + @@ -66,8 +66,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/R/docs/pubchem_graphjson.html b/Rscript/Library/mzkit_app/vignettes/R/docs/pubchem_graphjson.html index eeb9a843cf..9759ac7104 100644 --- a/Rscript/Library/mzkit_app/vignettes/R/docs/pubchem_graphjson.html +++ b/Rscript/Library/mzkit_app/vignettes/R/docs/pubchem_graphjson.html @@ -5,7 +5,7 @@ Parse the pugview xml as the metabolite data object - + @@ -73,8 +73,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/R/docs/pubchem_meta.html b/Rscript/Library/mzkit_app/vignettes/R/docs/pubchem_meta.html index bf3d4d39ef..69c6e16102 100644 --- a/Rscript/Library/mzkit_app/vignettes/R/docs/pubchem_meta.html +++ b/Rscript/Library/mzkit_app/vignettes/R/docs/pubchem_meta.html @@ -5,7 +5,7 @@ Helper script for run pubchem database query - + @@ -63,8 +63,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/R/docs/run.Deconvolution.html b/Rscript/Library/mzkit_app/vignettes/R/docs/run.Deconvolution.html index 3bbe1f7080..8870606ae7 100644 --- a/Rscript/Library/mzkit_app/vignettes/R/docs/run.Deconvolution.html +++ b/Rscript/Library/mzkit_app/vignettes/R/docs/run.Deconvolution.html @@ -5,7 +5,7 @@ Do ms1 deconvolution of the rawdata - + @@ -93,8 +93,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/R/docs/tolerance.html b/Rscript/Library/mzkit_app/vignettes/R/docs/tolerance.html index a730b55dd9..2b4b04bfc8 100644 --- a/Rscript/Library/mzkit_app/vignettes/R/docs/tolerance.html +++ b/Rscript/Library/mzkit_app/vignettes/R/docs/tolerance.html @@ -5,7 +5,7 @@ Create mzdiff tolerance value - + @@ -69,8 +69,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/.html b/Rscript/Library/mzkit_app/vignettes/clr/.html index c116d85cc5..a07012fda8 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/.html @@ -5,7 +5,7 @@ - + @@ -46,8 +46,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/ASCII/MGF/Ions.html b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/ASCII/MGF/Ions.html index 594620a621..9c22f2f71c 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/ASCII/MGF/Ions.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/ASCII/MGF/Ions.html @@ -5,7 +5,7 @@ BioNovoGene.Analytical.MassSpectrometry.Assembly.ASCII.MGF.Ions - + @@ -71,8 +71,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/ASCII/MSL/MSLIon.html b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/ASCII/MSL/MSLIon.html index 07f452b838..5f8ad76cc3 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/ASCII/MSL/MSLIon.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/ASCII/MSL/MSLIon.html @@ -5,7 +5,7 @@ BioNovoGene.Analytical.MassSpectrometry.Assembly.ASCII.MSL.MSLIon - + @@ -62,8 +62,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/ASCII/MSP/MspData.html b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/ASCII/MSP/MspData.html index ceb3bc8024..8bce007e56 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/ASCII/MSP/MspData.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/ASCII/MSP/MspData.html @@ -5,7 +5,7 @@ BioNovoGene.Analytical.MassSpectrometry.Assembly.ASCII.MSP.MspData - + @@ -71,8 +71,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/ASCII/Raman/Spectroscopy.html b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/ASCII/Raman/Spectroscopy.html index c800eb96fd..0ddc68cef6 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/ASCII/Raman/Spectroscopy.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/ASCII/Raman/Spectroscopy.html @@ -5,7 +5,7 @@ BioNovoGene.Analytical.MassSpectrometry.Assembly.ASCII.Raman.Spectroscopy - + @@ -73,8 +73,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/AnnotationWorkspace.html b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/AnnotationWorkspace.html index f600cbfbea..da8331a14b 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/AnnotationWorkspace.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/AnnotationWorkspace.html @@ -5,7 +5,7 @@ BioNovoGene.Analytical.MassSpectrometry.Assembly.AnnotationWorkspace - + @@ -48,8 +48,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/Comprehensive/D2Chromatogram.html b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/Comprehensive/D2Chromatogram.html index 3dc02bbf8a..a1a1aa133d 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/Comprehensive/D2Chromatogram.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/Comprehensive/D2Chromatogram.html @@ -5,7 +5,7 @@ BioNovoGene.Analytical.MassSpectrometry.Assembly.Comprehensive.D2Chromatogram - + @@ -56,8 +56,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/Comprehensive/MsImaging/Correction.html b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/Comprehensive/MsImaging/Correction.html index bf1d02ad67..9ccbe85158 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/Comprehensive/MsImaging/Correction.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/Comprehensive/MsImaging/Correction.html @@ -5,7 +5,7 @@ BioNovoGene.Analytical.MassSpectrometry.Assembly.Comprehensive.MsImaging.Correction - + @@ -46,8 +46,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/Comprehensive/MsImaging/Metadata.html b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/Comprehensive/MsImaging/Metadata.html index 8f23bf5b50..7e8ff9f469 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/Comprehensive/MsImaging/Metadata.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/Comprehensive/MsImaging/Metadata.html @@ -5,7 +5,7 @@ BioNovoGene.Analytical.MassSpectrometry.Assembly.Comprehensive.MsImaging.Metadata - + @@ -65,8 +65,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/Comprehensive/MsImaging/ScanMs2Correction.html b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/Comprehensive/MsImaging/ScanMs2Correction.html index b2e4e717dc..a879493ad7 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/Comprehensive/MsImaging/ScanMs2Correction.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/Comprehensive/MsImaging/ScanMs2Correction.html @@ -5,7 +5,7 @@ BioNovoGene.Analytical.MassSpectrometry.Assembly.Comprehensive.MsImaging.ScanMs2Correction - + @@ -48,8 +48,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/Comprehensive/MsImaging/ScanTimeCorrection.html b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/Comprehensive/MsImaging/ScanTimeCorrection.html index 6cac1e09b5..e467b65da5 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/Comprehensive/MsImaging/ScanTimeCorrection.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/Comprehensive/MsImaging/ScanTimeCorrection.html @@ -5,7 +5,7 @@ BioNovoGene.Analytical.MassSpectrometry.Assembly.Comprehensive.MsImaging.ScanTimeCorrection - + @@ -52,8 +52,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MZWork/WorkspaceAccess.html b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MZWork/WorkspaceAccess.html index f4a405d8dd..a28aaccb9b 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MZWork/WorkspaceAccess.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MZWork/WorkspaceAccess.html @@ -5,7 +5,7 @@ BioNovoGene.Analytical.MassSpectrometry.Assembly.MZWork.WorkspaceAccess - + @@ -46,8 +46,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/FastSeekIndex.html b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/FastSeekIndex.html index c77ab5a69b..010f7bfba7 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/FastSeekIndex.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/FastSeekIndex.html @@ -5,7 +5,7 @@ BioNovoGene.Analytical.MassSpectrometry.Assembly.MarkupData.FastSeekIndex - + @@ -61,8 +61,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/XmlSeek.html b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/XmlSeek.html index 7e12e80b63..20e0ac6791 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/XmlSeek.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/XmlSeek.html @@ -5,7 +5,7 @@ BioNovoGene.Analytical.MassSpectrometry.Assembly.MarkupData.XmlSeek - + @@ -47,8 +47,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/imzML/IntensitySummary.html b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/imzML/IntensitySummary.html index 6b8b8119a6..8f864dc0c6 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/imzML/IntensitySummary.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/imzML/IntensitySummary.html @@ -5,7 +5,7 @@ BioNovoGene.Analytical.MassSpectrometry.Assembly.MarkupData.imzML.IntensitySummary - + @@ -63,8 +63,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/imzML/MSISummary.html b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/imzML/MSISummary.html index 24e7775ed1..ff79bd7161 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/imzML/MSISummary.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/imzML/MSISummary.html @@ -5,7 +5,7 @@ BioNovoGene.Analytical.MassSpectrometry.Assembly.MarkupData.imzML.MSISummary - + @@ -60,8 +60,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/imzML/PixelScanIntensity.html b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/imzML/PixelScanIntensity.html index 2852755d7b..f1deb9e19c 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/imzML/PixelScanIntensity.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Assembly/MarkupData/imzML/PixelScanIntensity.html @@ -5,7 +5,7 @@ BioNovoGene.Analytical.MassSpectrometry.Assembly.MarkupData.imzML.PixelScanIntensity - + @@ -52,8 +52,8 @@

.NET clr type reference tree

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- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/MoleculeNetworking/NetworkingNode.html b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/MoleculeNetworking/NetworkingNode.html index 9f1deed347..bd4812c12c 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/MoleculeNetworking/NetworkingNode.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/MoleculeNetworking/NetworkingNode.html @@ -5,7 +5,7 @@ BioNovoGene.Analytical.MassSpectrometry.Math.Spectra.MoleculeNetworking.NetworkingNode - + @@ -57,8 +57,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/MzIndex.html b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/MzIndex.html index f473e0a628..b27ed2dc87 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/MzIndex.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/MzIndex.html @@ -5,7 +5,7 @@ BioNovoGene.Analytical.MassSpectrometry.Math.Spectra.MzIndex - + @@ -51,8 +51,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/MzPool.html b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/MzPool.html index 18946c5cd4..2c98c1e553 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/MzPool.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/MzPool.html @@ -5,7 +5,7 @@ BioNovoGene.Analytical.MassSpectrometry.Math.Spectra.MzPool - + @@ -58,8 +58,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/PeakList.html b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/PeakList.html index 40d47175ae..d58320fac2 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/PeakList.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/PeakList.html @@ -5,7 +5,7 @@ BioNovoGene.Analytical.MassSpectrometry.Math.Spectra.PeakList - + @@ -61,8 +61,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/PeakMs2.html b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/PeakMs2.html index 79695ae865..779fd7d19c 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/PeakMs2.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/PeakMs2.html @@ -5,7 +5,7 @@ BioNovoGene.Analytical.MassSpectrometry.Math.Spectra.PeakMs2 - + @@ -77,8 +77,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/PeakQuality.html b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/PeakQuality.html index bbbc9f996c..b77a854f50 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/PeakQuality.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/PeakQuality.html @@ -5,7 +5,7 @@ BioNovoGene.Analytical.MassSpectrometry.Math.Spectra.PeakQuality - + @@ -60,8 +60,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/ScoreAggregates.html b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/ScoreAggregates.html index 4e94ea17dd..22a834b59b 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/ScoreAggregates.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/ScoreAggregates.html @@ -5,7 +5,7 @@ BioNovoGene.Analytical.MassSpectrometry.Math.Spectra.ScoreAggregates - + @@ -57,8 +57,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/SpectrumCluster.html b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/SpectrumCluster.html index 29ca804b9c..606f38c0be 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/SpectrumCluster.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/SpectrumCluster.html @@ -5,7 +5,7 @@ BioNovoGene.Analytical.MassSpectrometry.Math.Spectra.SpectrumCluster - + @@ -58,8 +58,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/SpectrumComment.html b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/SpectrumComment.html index 0d2336c77a..a4e91f74bb 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/SpectrumComment.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/SpectrumComment.html @@ -5,7 +5,7 @@ BioNovoGene.Analytical.MassSpectrometry.Math.Spectra.SpectrumComment - + @@ -123,8 +123,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/SpectrumPeak.html b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/SpectrumPeak.html index 3e9f00b9f5..80737ee522 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/SpectrumPeak.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/SpectrumPeak.html @@ -5,7 +5,7 @@ BioNovoGene.Analytical.MassSpectrometry.Math.Spectra.SpectrumPeak - + @@ -65,8 +65,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/SpectrumTreeCluster.html b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/SpectrumTreeCluster.html index abd422abfc..fcaa93c3fa 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/SpectrumTreeCluster.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/SpectrumTreeCluster.html @@ -5,7 +5,7 @@ BioNovoGene.Analytical.MassSpectrometry.Math.Spectra.SpectrumTreeCluster - + @@ -61,8 +61,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/Xml/AlignmentOutput.html b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/Xml/AlignmentOutput.html index 882b7e2ef5..b3fb181304 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/Xml/AlignmentOutput.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/Xml/AlignmentOutput.html @@ -5,7 +5,7 @@ BioNovoGene.Analytical.MassSpectrometry.Math.Spectra.Xml.AlignmentOutput - + @@ -22,7 +22,9 @@

AlignmentOutput

Description

- +

the spectrum similarity comparision result object

+ +

contains the score and spectrum fragment alignment details result data.

Declare

@@ -34,8 +36,11 @@

Declare

alignments: SSM2MatrixFragment[]; # the min value of AlignmentOutput.forward and AlignmentOutput.reverse cosine: double; + # the spectrum entropy similarity entropy: double; + # the forward cosine score forward: double; + # the jaccard index between the fragment set of query vs subject jaccard: double; # get score mean result mean: double; @@ -43,6 +48,7 @@

Declare

nhits: integer; query: Meta; reference: Meta; + # the reverse cosine score reverse: double; } @@ -64,8 +70,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/Xml/Meta.html b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/Xml/Meta.html index ecc163f959..e43039ed82 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/Xml/Meta.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/Xml/Meta.html @@ -5,7 +5,7 @@ BioNovoGene.Analytical.MassSpectrometry.Math.Spectra.Xml.Meta - + @@ -52,8 +52,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/Xml/SSM2MatrixFragment.html b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/Xml/SSM2MatrixFragment.html index 86b715bcb2..5b474afcf9 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/Xml/SSM2MatrixFragment.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/Xml/SSM2MatrixFragment.html @@ -5,7 +5,7 @@ BioNovoGene.Analytical.MassSpectrometry.Math.Spectra.Xml.SSM2MatrixFragment - + @@ -54,8 +54,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/ms2.html b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/ms2.html index 91d582d0a2..785f6a96aa 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/ms2.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/Spectra/ms2.html @@ -5,7 +5,7 @@ BioNovoGene.Analytical.MassSpectrometry.Math.Spectra.ms2 - + @@ -61,8 +61,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/XICPool.html b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/XICPool.html index 34d5b4b4b1..f87ede41ed 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/XICPool.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/XICPool.html @@ -5,7 +5,7 @@ BioNovoGene.Analytical.MassSpectrometry.Math.XICPool - + @@ -46,8 +46,8 @@

.NET clr type reference tree

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.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/ms1_scan.html b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/ms1_scan.html index a2e40453de..bf2053ca2f 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/ms1_scan.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/ms1_scan.html @@ -5,7 +5,7 @@ BioNovoGene.Analytical.MassSpectrometry.Math.ms1_scan - + @@ -51,8 +51,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/ms1_scan[].html b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/ms1_scan[].html index 54b5593034..dc04622df1 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/ms1_scan[].html +++ b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/ms1_scan[].html @@ -5,7 +5,7 @@ BioNovoGene.Analytical.MassSpectrometry.Math.ms1_scan[] - + @@ -56,8 +56,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/xcms2.html b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/xcms2.html index b67ae56b22..3c9bfe497a 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/xcms2.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/Math/xcms2.html @@ -5,7 +5,7 @@ BioNovoGene.Analytical.MassSpectrometry.Math.xcms2 - + @@ -68,8 +68,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/MsImaging/Blender/QuantizationThreshold.html b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/MsImaging/Blender/QuantizationThreshold.html index de831b99fd..8956e32d5e 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/MsImaging/Blender/QuantizationThreshold.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/MsImaging/Blender/QuantizationThreshold.html @@ -5,7 +5,7 @@ BioNovoGene.Analytical.MassSpectrometry.MsImaging.Blender.QuantizationThreshold - + @@ -47,8 +47,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/MsImaging/Blender/Scaler/DenoiseScaler.html b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/MsImaging/Blender/Scaler/DenoiseScaler.html index d8bd9c8369..0bcc61469d 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/MsImaging/Blender/Scaler/DenoiseScaler.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/MsImaging/Blender/Scaler/DenoiseScaler.html @@ -5,7 +5,7 @@ BioNovoGene.Analytical.MassSpectrometry.MsImaging.Blender.Scaler.DenoiseScaler - + @@ -50,8 +50,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/MsImaging/Blender/Scaler/KNNScaler.html b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/MsImaging/Blender/Scaler/KNNScaler.html index a8db322c07..0035845f93 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/MsImaging/Blender/Scaler/KNNScaler.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/MsImaging/Blender/Scaler/KNNScaler.html @@ -5,7 +5,7 @@ BioNovoGene.Analytical.MassSpectrometry.MsImaging.Blender.Scaler.KNNScaler - + @@ -51,8 +51,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/MsImaging/Blender/Scaler/RasterPipeline.html b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/MsImaging/Blender/Scaler/RasterPipeline.html index 32abac925e..352fd115d9 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/MsImaging/Blender/Scaler/RasterPipeline.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/MsImaging/Blender/Scaler/RasterPipeline.html @@ -5,7 +5,7 @@ BioNovoGene.Analytical.MassSpectrometry.MsImaging.Blender.Scaler.RasterPipeline - + @@ -46,8 +46,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/MsImaging/Blender/Scaler/Scaler+LayerScaler.html b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/MsImaging/Blender/Scaler/Scaler+LayerScaler.html index 27c3b69753..22cab0c6c1 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/MsImaging/Blender/Scaler/Scaler+LayerScaler.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/MsImaging/Blender/Scaler/Scaler+LayerScaler.html @@ -5,7 +5,7 @@ BioNovoGene.Analytical.MassSpectrometry.MsImaging.Blender.Scaler.Scaler+LayerScaler - + @@ -46,8 +46,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/MsImaging/Blender/Scaler/Scaler.html b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/MsImaging/Blender/Scaler/Scaler.html index 02d8db4ddd..65c9ebf1c1 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/MsImaging/Blender/Scaler/Scaler.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/MsImaging/Blender/Scaler/Scaler.html @@ -5,7 +5,7 @@ BioNovoGene.Analytical.MassSpectrometry.MsImaging.Blender.Scaler.Scaler - + @@ -46,8 +46,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/MsImaging/Blender/Scaler/SoftenScaler.html b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/MsImaging/Blender/Scaler/SoftenScaler.html index 8b825c278e..8fcde0455c 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/MsImaging/Blender/Scaler/SoftenScaler.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/Analytical/MassSpectrometry/MsImaging/Blender/Scaler/SoftenScaler.html @@ -5,7 +5,7 @@ BioNovoGene.Analytical.MassSpectrometry.MsImaging.Blender.Scaler.SoftenScaler - + @@ -48,8 +48,8 @@

.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/BioDeep/MetaDNA/CompoundSolver.html b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/BioDeep/MetaDNA/CompoundSolver.html index c0a6052ce9..af83160c60 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/BioDeep/MetaDNA/CompoundSolver.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/BioDeep/MetaDNA/CompoundSolver.html @@ -5,7 +5,7 @@ BioNovoGene.BioDeep.MetaDNA.CompoundSolver - + @@ -52,8 +52,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/BioDeep/MetaDNA/Infer/Candidate.html b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/BioDeep/MetaDNA/Infer/Candidate.html index 897eb4a7c5..79451a4f03 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/BioDeep/MetaDNA/Infer/Candidate.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/BioDeep/MetaDNA/Infer/Candidate.html @@ -5,7 +5,7 @@ BioNovoGene.BioDeep.MetaDNA.Infer.Candidate - + @@ -56,8 +56,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/BioDeep/MetaDNA/Infer/CandidateInfer.html b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/BioDeep/MetaDNA/Infer/CandidateInfer.html index 69d1d1069f..6a161aef2f 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/BioDeep/MetaDNA/Infer/CandidateInfer.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/BioDeep/MetaDNA/Infer/CandidateInfer.html @@ -5,7 +5,7 @@ BioNovoGene.BioDeep.MetaDNA.Infer.CandidateInfer - + @@ -50,8 +50,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/BioDeep/MetaDNA/Infer/InferLevel.html b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/BioDeep/MetaDNA/Infer/InferLevel.html index d73b84471b..841c8f7610 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/BioDeep/MetaDNA/Infer/InferLevel.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/BioDeep/MetaDNA/Infer/InferLevel.html @@ -5,7 +5,7 @@ BioNovoGene.BioDeep.MetaDNA.Infer.InferLevel - + @@ -54,8 +54,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/BioDeep/MetaDNA/Infer/InferLink.html b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/BioDeep/MetaDNA/Infer/InferLink.html index 23cfc743d1..fd642a0a69 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/BioDeep/MetaDNA/Infer/InferLink.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/BioDeep/MetaDNA/Infer/InferLink.html @@ -5,7 +5,7 @@ BioNovoGene.BioDeep.MetaDNA.Infer.InferLink - + @@ -74,8 +74,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/BioDeep/MetaDNA/MetaDNARawSet.html b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/BioDeep/MetaDNA/MetaDNARawSet.html index ffe265cbfa..623076e359 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/BioDeep/MetaDNA/MetaDNARawSet.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/BioDeep/MetaDNA/MetaDNARawSet.html @@ -5,7 +5,7 @@ BioNovoGene.BioDeep.MetaDNA.MetaDNARawSet - + @@ -53,8 +53,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/BioDeep/MetaDNA/MetaDNAResult.html b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/BioDeep/MetaDNA/MetaDNAResult.html index 4f8a176fd1..ce07fb1ff7 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/BioDeep/MetaDNA/MetaDNAResult.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/BioDeep/MetaDNA/MetaDNAResult.html @@ -5,7 +5,7 @@ BioNovoGene.BioDeep.MetaDNA.MetaDNAResult - + @@ -88,8 +88,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/BioDeep/MetaDNA/Networking.html b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/BioDeep/MetaDNA/Networking.html index b4c337cd56..fb72da2b95 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/BioDeep/MetaDNA/Networking.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/BioDeep/MetaDNA/Networking.html @@ -5,7 +5,7 @@ BioNovoGene.BioDeep.MetaDNA.Networking - + @@ -46,8 +46,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/BioDeep/MetaDNA/OntologyTree.html b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/BioDeep/MetaDNA/OntologyTree.html index 0f572bbc1d..7ca3ca54c5 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/BioDeep/MetaDNA/OntologyTree.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/BioDeep/MetaDNA/OntologyTree.html @@ -5,7 +5,7 @@ BioNovoGene.BioDeep.MetaDNA.OntologyTree - + @@ -48,8 +48,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/BioDeep/MetaDNA/Visual/ReactionClass.html b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/BioDeep/MetaDNA/Visual/ReactionClass.html index 24478781b9..51781bd8ea 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/BioDeep/MetaDNA/Visual/ReactionClass.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/BioNovoGene/BioDeep/MetaDNA/Visual/ReactionClass.html @@ -5,7 +5,7 @@ BioNovoGene.BioDeep.MetaDNA.Visual.ReactionClass - + @@ -51,8 +51,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/ApplicationServices/Debugging/Diagnostics/Method.html b/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/ApplicationServices/Debugging/Diagnostics/Method.html index 6ae25c0dca..b897fd66e8 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/ApplicationServices/Debugging/Diagnostics/Method.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/ApplicationServices/Debugging/Diagnostics/Method.html @@ -5,7 +5,7 @@ Microsoft.VisualBasic.ApplicationServices.Debugging.Diagnostics.Method - + @@ -49,8 +49,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/ApplicationServices/Debugging/Diagnostics/StackFrame.html b/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/ApplicationServices/Debugging/Diagnostics/StackFrame.html index 8060243652..f8854d45f1 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/ApplicationServices/Debugging/Diagnostics/StackFrame.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/ApplicationServices/Debugging/Diagnostics/StackFrame.html @@ -5,7 +5,7 @@ Microsoft.VisualBasic.ApplicationServices.Debugging.Diagnostics.StackFrame - + @@ -55,8 +55,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/ApplicationServices/Debugging/Logging/MSG_TYPES.html b/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/ApplicationServices/Debugging/Logging/MSG_TYPES.html index 235751dc5d..5b4a27c861 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/ApplicationServices/Debugging/Logging/MSG_TYPES.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/ApplicationServices/Debugging/Logging/MSG_TYPES.html @@ -5,7 +5,7 @@ Microsoft.VisualBasic.ApplicationServices.Debugging.Logging.MSG_TYPES - + @@ -72,8 +72,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/ApplicationServices/Development/AssemblyInfo.html b/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/ApplicationServices/Development/AssemblyInfo.html index d8566053c9..83118d542b 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/ApplicationServices/Development/AssemblyInfo.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/ApplicationServices/Development/AssemblyInfo.html @@ -5,7 +5,7 @@ Microsoft.VisualBasic.ApplicationServices.Development.AssemblyInfo - + @@ -65,8 +65,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/ApplicationServices/Development/XmlDoc/Assembly/Project.html b/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/ApplicationServices/Development/XmlDoc/Assembly/Project.html index 94136b385a..6f9f32f29f 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/ApplicationServices/Development/XmlDoc/Assembly/Project.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/ApplicationServices/Development/XmlDoc/Assembly/Project.html @@ -5,7 +5,7 @@ Microsoft.VisualBasic.ApplicationServices.Development.XmlDoc.Assembly.Project - + @@ -50,8 +50,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/ApplicationServices/Development/XmlDoc/Assembly/ProjectNamespace.html b/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/ApplicationServices/Development/XmlDoc/Assembly/ProjectNamespace.html index 8aeac5f1ad..1f5f748958 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/ApplicationServices/Development/XmlDoc/Assembly/ProjectNamespace.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/ApplicationServices/Development/XmlDoc/Assembly/ProjectNamespace.html @@ -5,7 +5,7 @@ Microsoft.VisualBasic.ApplicationServices.Development.XmlDoc.Assembly.ProjectNamespace - + @@ -50,8 +50,8 @@

.NET clr type reference tree

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.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/ApplicationServices/Development/XmlDoc/Assembly/XmlDocs.html b/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/ApplicationServices/Development/XmlDoc/Assembly/XmlDocs.html index 0426bdbeff..46de487505 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/ApplicationServices/Development/XmlDoc/Assembly/XmlDocs.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/ApplicationServices/Development/XmlDoc/Assembly/XmlDocs.html @@ -5,7 +5,7 @@ Microsoft.VisualBasic.ApplicationServices.Development.XmlDoc.Assembly.XmlDocs - + @@ -57,8 +57,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/CommandLine/ExecuteEmptyCLI.html b/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/CommandLine/ExecuteEmptyCLI.html index 40e92a094d..5c4a314b04 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/CommandLine/ExecuteEmptyCLI.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/CommandLine/ExecuteEmptyCLI.html @@ -5,7 +5,7 @@ Microsoft.VisualBasic.CommandLine.ExecuteEmptyCLI - + @@ -52,8 +52,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/CommandLine/ExecuteFile.html b/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/CommandLine/ExecuteFile.html index f2983bebb3..988fe018be 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/CommandLine/ExecuteFile.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/CommandLine/ExecuteFile.html @@ -5,7 +5,7 @@ Microsoft.VisualBasic.CommandLine.ExecuteFile - + @@ -52,8 +52,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/CommandLine/ExecuteNotFound.html b/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/CommandLine/ExecuteNotFound.html index 322f3c88c0..21c3a04840 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/CommandLine/ExecuteNotFound.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/CommandLine/ExecuteNotFound.html @@ -5,7 +5,7 @@ Microsoft.VisualBasic.CommandLine.ExecuteNotFound - + @@ -52,8 +52,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/CommandLine/ExecuteQuery.html b/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/CommandLine/ExecuteQuery.html index 999228ea7b..0aca5767ac 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/CommandLine/ExecuteQuery.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/CommandLine/ExecuteQuery.html @@ -5,7 +5,7 @@ Microsoft.VisualBasic.CommandLine.ExecuteQuery - + @@ -52,8 +52,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/CommandLine/Interpreter.html b/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/CommandLine/Interpreter.html index 438d745689..3e59e4a048 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/CommandLine/Interpreter.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/CommandLine/Interpreter.html @@ -5,7 +5,7 @@ Microsoft.VisualBasic.CommandLine.Interpreter - + @@ -82,8 +82,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/CommandLine/Reflection/ArgumentCollection.html b/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/CommandLine/Reflection/ArgumentCollection.html index 5be1c865c7..764ca8f4d2 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/CommandLine/Reflection/ArgumentCollection.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/CommandLine/Reflection/ArgumentCollection.html @@ -5,7 +5,7 @@ Microsoft.VisualBasic.CommandLine.Reflection.ArgumentCollection - + @@ -53,8 +53,8 @@

.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/Imaging/IGraphics.html b/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/Imaging/IGraphics.html index 99e1585eaa..de62358ddd 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/Imaging/IGraphics.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/Imaging/IGraphics.html @@ -5,7 +5,7 @@ Microsoft.VisualBasic.Imaging.IGraphics - + @@ -76,8 +76,8 @@

.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/Imaging/SVG/XML/Enums/SvgEnum.html b/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/Imaging/SVG/XML/Enums/SvgEnum.html index a738f363ab..7bdb2a3abc 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/Imaging/SVG/XML/Enums/SvgEnum.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/Imaging/SVG/XML/Enums/SvgEnum.html @@ -5,7 +5,7 @@ Microsoft.VisualBasic.Imaging.SVG.XML.Enums.SvgEnum - + @@ -46,8 +46,8 @@

.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/Math/LinearAlgebra/Matrix/SparseMatrix.html b/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/Math/LinearAlgebra/Matrix/SparseMatrix.html index db22ba5c6a..744c85435a 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/Math/LinearAlgebra/Matrix/SparseMatrix.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/Math/LinearAlgebra/Matrix/SparseMatrix.html @@ -5,7 +5,7 @@ Microsoft.VisualBasic.Math.LinearAlgebra.Matrix.SparseMatrix - + @@ -48,8 +48,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/Math/LinearAlgebra/Vector.html b/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/Math/LinearAlgebra/Vector.html index 7a2ba431c1..22b73ddf96 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/Math/LinearAlgebra/Vector.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/Math/LinearAlgebra/Vector.html @@ -5,7 +5,7 @@ Microsoft.VisualBasic.Math.LinearAlgebra.Vector - + @@ -74,8 +74,8 @@

.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/Math/Statistics/Hypothesis/FishersExact/FishersExactPvalues.html b/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/Math/Statistics/Hypothesis/FishersExact/FishersExactPvalues.html index 99a57bfdf0..17ad03734b 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/Math/Statistics/Hypothesis/FishersExact/FishersExactPvalues.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/Microsoft/VisualBasic/Math/Statistics/Hypothesis/FishersExact/FishersExactPvalues.html @@ -5,7 +5,7 @@ Microsoft.VisualBasic.Math.Statistics.Hypothesis.FishersExact.FishersExactPvalues - + @@ -61,8 +61,8 @@

.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Development/AnnotationDocs.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Development/AnnotationDocs.html index 8e220a1624..217401b21d 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Development/AnnotationDocs.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Development/AnnotationDocs.html @@ -5,7 +5,7 @@ SMRUCC.Rsharp.Development.AnnotationDocs - + @@ -46,8 +46,8 @@

.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Development/Configuration/StartupConfigs.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Development/Configuration/StartupConfigs.html index efa40e5e91..b5c264c83a 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Development/Configuration/StartupConfigs.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Development/Configuration/StartupConfigs.html @@ -5,7 +5,7 @@ SMRUCC.Rsharp.Development.Configuration.StartupConfigs - + @@ -47,8 +47,8 @@

.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Development/Package/Package.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Development/Package/Package.html index 52979ce882..8487203b5b 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Development/Package/Package.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Development/Package/Package.html @@ -5,7 +5,7 @@ SMRUCC.Rsharp.Development.Package.Package - + @@ -62,8 +62,8 @@

.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

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.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Interpreter/ExecuteEngine/ExpressionSymbols/Closure/ClosureExpression.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Interpreter/ExecuteEngine/ExpressionSymbols/Closure/ClosureExpression.html index 91d2a2f8e1..ca39c68e46 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Interpreter/ExecuteEngine/ExpressionSymbols/Closure/ClosureExpression.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Interpreter/ExecuteEngine/ExpressionSymbols/Closure/ClosureExpression.html @@ -5,7 +5,7 @@ SMRUCC.Rsharp.Interpreter.ExecuteEngine.ExpressionSymbols.Closure.ClosureExpression - + @@ -57,8 +57,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Interpreter/ExecuteEngine/ExpressionSymbols/Closure/DeclareLambdaFunction.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Interpreter/ExecuteEngine/ExpressionSymbols/Closure/DeclareLambdaFunction.html index 0ac95c0e9c..da0308fcd3 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Interpreter/ExecuteEngine/ExpressionSymbols/Closure/DeclareLambdaFunction.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Interpreter/ExecuteEngine/ExpressionSymbols/Closure/DeclareLambdaFunction.html @@ -5,7 +5,7 @@ SMRUCC.Rsharp.Interpreter.ExecuteEngine.ExpressionSymbols.Closure.DeclareLambdaFunction - + @@ -65,8 +65,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Interpreter/ExecuteEngine/ExpressionSymbols/Closure/DeclareNewFunction.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Interpreter/ExecuteEngine/ExpressionSymbols/Closure/DeclareNewFunction.html index 1bd61a17f4..4615415e34 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Interpreter/ExecuteEngine/ExpressionSymbols/Closure/DeclareNewFunction.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Interpreter/ExecuteEngine/ExpressionSymbols/Closure/DeclareNewFunction.html @@ -5,7 +5,7 @@ SMRUCC.Rsharp.Interpreter.ExecuteEngine.ExpressionSymbols.Closure.DeclareNewFunction - + @@ -96,8 +96,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Interpreter/ExecuteEngine/ExpressionSymbols/Closure/DeclareNewSymbol.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Interpreter/ExecuteEngine/ExpressionSymbols/Closure/DeclareNewSymbol.html index ebcf3940a5..e25eed5fee 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Interpreter/ExecuteEngine/ExpressionSymbols/Closure/DeclareNewSymbol.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Interpreter/ExecuteEngine/ExpressionSymbols/Closure/DeclareNewSymbol.html @@ -5,7 +5,7 @@ SMRUCC.Rsharp.Interpreter.ExecuteEngine.ExpressionSymbols.Closure.DeclareNewSymbol - + @@ -71,8 +71,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Interpreter/ExecuteEngine/ExpressionSymbols/Closure/UsingClosure.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Interpreter/ExecuteEngine/ExpressionSymbols/Closure/UsingClosure.html index 32a9bce0a9..2426326740 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Interpreter/ExecuteEngine/ExpressionSymbols/Closure/UsingClosure.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Interpreter/ExecuteEngine/ExpressionSymbols/Closure/UsingClosure.html @@ -5,7 +5,7 @@ SMRUCC.Rsharp.Interpreter.ExecuteEngine.ExpressionSymbols.Closure.UsingClosure - + @@ -61,8 +61,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Interpreter/ExecuteEngine/SymbolExpression.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Interpreter/ExecuteEngine/SymbolExpression.html index 4393b51460..97202d34bd 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Interpreter/ExecuteEngine/SymbolExpression.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Interpreter/ExecuteEngine/SymbolExpression.html @@ -5,7 +5,7 @@ SMRUCC.Rsharp.Interpreter.ExecuteEngine.SymbolExpression - + @@ -60,8 +60,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Interpreter/RInterpreter.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Interpreter/RInterpreter.html index 4e78ae280a..88acaccce1 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Interpreter/RInterpreter.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Interpreter/RInterpreter.html @@ -5,7 +5,7 @@ SMRUCC.Rsharp.Interpreter.RInterpreter - + @@ -67,8 +67,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Components/Interface/RFunction.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Components/Interface/RFunction.html index a52fdaa919..5ef220efb9 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Components/Interface/RFunction.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Components/Interface/RFunction.html @@ -5,7 +5,7 @@ SMRUCC.Rsharp.Runtime.Components.Interface.RFunction - + @@ -52,8 +52,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Components/Message.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Components/Message.html index 9789b34141..6b00d7219e 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Components/Message.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Components/Message.html @@ -5,7 +5,7 @@ SMRUCC.Rsharp.Runtime.Components.Message - + @@ -61,8 +61,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Components/RsharpDataObject.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Components/RsharpDataObject.html index 924fa5238b..8dfbbd24d5 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Components/RsharpDataObject.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Components/RsharpDataObject.html @@ -5,7 +5,7 @@ SMRUCC.Rsharp.Runtime.Components.RsharpDataObject - + @@ -49,8 +49,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Components/Symbol.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Components/Symbol.html index 59051516e4..bc039173ea 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Components/Symbol.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Components/Symbol.html @@ -5,7 +5,7 @@ SMRUCC.Rsharp.Runtime.Components.Symbol - + @@ -73,8 +73,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Components/TypeCodes.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Components/TypeCodes.html index a4569cd307..73cd25dfc8 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Components/TypeCodes.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Components/TypeCodes.html @@ -5,7 +5,7 @@ SMRUCC.Rsharp.Runtime.Components.TypeCodes - + @@ -99,8 +99,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Environment.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Environment.html index ff52b3db79..590f2503c7 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Environment.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Environment.html @@ -5,7 +5,7 @@ SMRUCC.Rsharp.Runtime.Environment - + @@ -71,8 +71,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/GlobalEnvironment.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/GlobalEnvironment.html index de42daca27..b795cfdd70 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/GlobalEnvironment.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/GlobalEnvironment.html @@ -5,7 +5,7 @@ SMRUCC.Rsharp.Runtime.GlobalEnvironment - + @@ -99,8 +99,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Internal/Object/dataframe.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Internal/Object/dataframe.html index 4e023f068a..3d0b201762 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Internal/Object/dataframe.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Internal/Object/dataframe.html @@ -5,7 +5,7 @@ SMRUCC.Rsharp.Runtime.Internal.Object.dataframe - + @@ -134,8 +134,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Internal/Object/list.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Internal/Object/list.html index e9b01e2800..f26968d751 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Internal/Object/list.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Internal/Object/list.html @@ -5,7 +5,7 @@ SMRUCC.Rsharp.Runtime.Internal.Object.list - + @@ -57,8 +57,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Internal/Object/pipeline.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Internal/Object/pipeline.html index 212efdf77e..515406db88 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Internal/Object/pipeline.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Internal/Object/pipeline.html @@ -5,7 +5,7 @@ SMRUCC.Rsharp.Runtime.Internal.Object.pipeline - + @@ -63,8 +63,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Interop/IRType.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Interop/IRType.html index c6c7dcb7c1..07cea9d00b 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Interop/IRType.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Interop/IRType.html @@ -5,7 +5,7 @@ SMRUCC.Rsharp.Runtime.Interop.IRType - + @@ -53,8 +53,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Interop/RDefaultExpressionAttribute.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Interop/RDefaultExpressionAttribute.html index 3309c6d041..3bc001762a 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Interop/RDefaultExpressionAttribute.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Interop/RDefaultExpressionAttribute.html @@ -5,7 +5,7 @@ SMRUCC.Rsharp.Runtime.Interop.RDefaultExpressionAttribute - + @@ -63,8 +63,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Interop/RDefaultFunction.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Interop/RDefaultFunction.html index 3edb5bd189..84a2ca1abe 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Interop/RDefaultFunction.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Interop/RDefaultFunction.html @@ -5,7 +5,7 @@ SMRUCC.Rsharp.Runtime.Interop.RDefaultFunction - + @@ -46,8 +46,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Interop/RInteropAttribute.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Interop/RInteropAttribute.html index 47109e10cb..8df341bacd 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Interop/RInteropAttribute.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Interop/RInteropAttribute.html @@ -5,7 +5,7 @@ SMRUCC.Rsharp.Runtime.Interop.RInteropAttribute - + @@ -50,8 +50,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Interop/RMethodArgument.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Interop/RMethodArgument.html index 53118950d9..19f12f5279 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Interop/RMethodArgument.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Interop/RMethodArgument.html @@ -5,7 +5,7 @@ SMRUCC.Rsharp.Runtime.Interop.RMethodArgument - + @@ -65,8 +65,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Interop/RMethodInfo.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Interop/RMethodInfo.html index 6ef9babe87..0f9c4cbfde 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Interop/RMethodInfo.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Interop/RMethodInfo.html @@ -5,7 +5,7 @@ SMRUCC.Rsharp.Runtime.Interop.RMethodInfo - + @@ -65,8 +65,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Interop/RReturn.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Interop/RReturn.html index 68378a9aa3..53bfd62172 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Interop/RReturn.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Interop/RReturn.html @@ -5,7 +5,7 @@ SMRUCC.Rsharp.Runtime.Interop.RReturn - + @@ -58,8 +58,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Interop/RType.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Interop/RType.html index 00ba3c1ba2..977acb2d7a 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Interop/RType.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/Interop/RType.html @@ -5,7 +5,7 @@ SMRUCC.Rsharp.Runtime.Interop.RType - + @@ -71,8 +71,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/OutputEnvironments.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/OutputEnvironments.html index 028c47be17..a44fb3149a 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/OutputEnvironments.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/OutputEnvironments.html @@ -5,7 +5,7 @@ SMRUCC.Rsharp.Runtime.OutputEnvironments - + @@ -57,8 +57,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/RContentOutput.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/RContentOutput.html index 70e1f53ea6..82155cf869 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/RContentOutput.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/RContentOutput.html @@ -5,7 +5,7 @@ SMRUCC.Rsharp.Runtime.RContentOutput - + @@ -60,8 +60,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/SymbolLanguageProcessor.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/SymbolLanguageProcessor.html index 992f8a2f6a..305871a95e 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/SymbolLanguageProcessor.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/SymbolLanguageProcessor.html @@ -5,7 +5,7 @@ SMRUCC.Rsharp.Runtime.SymbolLanguageProcessor - + @@ -46,8 +46,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/SymbolNamespaceSolver.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/SymbolNamespaceSolver.html index 2534776b20..00f4a4ad9b 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/SymbolNamespaceSolver.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/Rsharp/Runtime/SymbolNamespaceSolver.html @@ -5,7 +5,7 @@ SMRUCC.Rsharp.Runtime.SymbolNamespaceSolver - + @@ -51,8 +51,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Analysis/HTS/DataFrame/DataFrameRow.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Analysis/HTS/DataFrame/DataFrameRow.html index 660a97b22f..d7a3f2b766 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Analysis/HTS/DataFrame/DataFrameRow.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Analysis/HTS/DataFrame/DataFrameRow.html @@ -5,7 +5,7 @@ SMRUCC.genomics.Analysis.HTS.DataFrame.DataFrameRow - + @@ -56,8 +56,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Analysis/HTS/DataFrame/Matrix.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Analysis/HTS/DataFrame/Matrix.html index 11eb5873e0..020d933d83 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Analysis/HTS/DataFrame/Matrix.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Analysis/HTS/DataFrame/Matrix.html @@ -5,7 +5,7 @@ SMRUCC.genomics.Analysis.HTS.DataFrame.Matrix - + @@ -60,8 +60,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Analysis/HTS/GSEA/Background.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Analysis/HTS/GSEA/Background.html index b5f5869ff5..7e65e5af45 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Analysis/HTS/GSEA/Background.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Analysis/HTS/GSEA/Background.html @@ -5,7 +5,7 @@ SMRUCC.genomics.Analysis.HTS.GSEA.Background - + @@ -66,8 +66,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Analysis/HTS/GSEA/BackgroundGene.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Analysis/HTS/GSEA/BackgroundGene.html index 9caea0765f..58f991b95a 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Analysis/HTS/GSEA/BackgroundGene.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Analysis/HTS/GSEA/BackgroundGene.html @@ -5,7 +5,7 @@ SMRUCC.genomics.Analysis.HTS.GSEA.BackgroundGene - + @@ -61,8 +61,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Analysis/HTS/GSEA/Cluster.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Analysis/HTS/GSEA/Cluster.html index e5431482ef..70b93d4191 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Analysis/HTS/GSEA/Cluster.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Analysis/HTS/GSEA/Cluster.html @@ -5,7 +5,7 @@ SMRUCC.genomics.Analysis.HTS.GSEA.Cluster - + @@ -61,8 +61,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/ELIXIR/EBI/ChEBI/XML/ChEBIEntity.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/ELIXIR/EBI/ChEBI/XML/ChEBIEntity.html index ac3585d10f..52859a51e0 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/ELIXIR/EBI/ChEBI/XML/ChEBIEntity.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/ELIXIR/EBI/ChEBI/XML/ChEBIEntity.html @@ -5,7 +5,7 @@ SMRUCC.genomics.Assembly.ELIXIR.EBI.ChEBI.XML.ChEBIEntity - + @@ -85,8 +85,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/ELIXIR/EBI/ChEBI/XML/ChemicalStructures.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/ELIXIR/EBI/ChEBI/XML/ChemicalStructures.html index f74a677bdd..4d90e762bc 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/ELIXIR/EBI/ChEBI/XML/ChemicalStructures.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/ELIXIR/EBI/ChEBI/XML/ChemicalStructures.html @@ -5,7 +5,7 @@ SMRUCC.genomics.Assembly.ELIXIR.EBI.ChEBI.XML.ChemicalStructures - + @@ -50,8 +50,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/ELIXIR/EBI/ChEBI/XML/CompoundOrigin.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/ELIXIR/EBI/ChEBI/XML/CompoundOrigin.html index 42ba289766..3982536df8 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/ELIXIR/EBI/ChEBI/XML/CompoundOrigin.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/ELIXIR/EBI/ChEBI/XML/CompoundOrigin.html @@ -5,7 +5,7 @@ SMRUCC.genomics.Assembly.ELIXIR.EBI.ChEBI.XML.CompoundOrigin - + @@ -52,8 +52,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/ELIXIR/EBI/ChEBI/XML/DatabaseLinks.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/ELIXIR/EBI/ChEBI/XML/DatabaseLinks.html index 18e2168129..061f822880 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/ELIXIR/EBI/ChEBI/XML/DatabaseLinks.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/ELIXIR/EBI/ChEBI/XML/DatabaseLinks.html @@ -5,7 +5,7 @@ SMRUCC.genomics.Assembly.ELIXIR.EBI.ChEBI.XML.DatabaseLinks - + @@ -48,8 +48,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/ELIXIR/EBI/ChEBI/XML/Formulae.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/ELIXIR/EBI/ChEBI/XML/Formulae.html index df60d3352e..afcb989995 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/ELIXIR/EBI/ChEBI/XML/Formulae.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/ELIXIR/EBI/ChEBI/XML/Formulae.html @@ -5,7 +5,7 @@ SMRUCC.genomics.Assembly.ELIXIR.EBI.ChEBI.XML.Formulae - + @@ -50,8 +50,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/ELIXIR/EBI/ChEBI/XML/OntologyParents.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/ELIXIR/EBI/ChEBI/XML/OntologyParents.html index 67bf0706b6..b0b4bc716f 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/ELIXIR/EBI/ChEBI/XML/OntologyParents.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/ELIXIR/EBI/ChEBI/XML/OntologyParents.html @@ -5,7 +5,7 @@ SMRUCC.genomics.Assembly.ELIXIR.EBI.ChEBI.XML.OntologyParents - + @@ -51,8 +51,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/ELIXIR/EBI/ChEBI/XML/RegistryNumbers.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/ELIXIR/EBI/ChEBI/XML/RegistryNumbers.html index 65c17adbd2..5e93351b1f 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/ELIXIR/EBI/ChEBI/XML/RegistryNumbers.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/ELIXIR/EBI/ChEBI/XML/RegistryNumbers.html @@ -5,7 +5,7 @@ SMRUCC.genomics.Assembly.ELIXIR.EBI.ChEBI.XML.RegistryNumbers - + @@ -49,8 +49,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/ELIXIR/EBI/ChEBI/XML/Synonyms.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/ELIXIR/EBI/ChEBI/XML/Synonyms.html index 18b97eaea2..bdbcaac47a 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/ELIXIR/EBI/ChEBI/XML/Synonyms.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/ELIXIR/EBI/ChEBI/XML/Synonyms.html @@ -5,7 +5,7 @@ SMRUCC.genomics.Assembly.ELIXIR.EBI.ChEBI.XML.Synonyms - + @@ -49,8 +49,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/Expasy/Database/Enzyme.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/Expasy/Database/Enzyme.html index 92b5202630..0d1b4b7da5 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/Expasy/Database/Enzyme.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/Expasy/Database/Enzyme.html @@ -5,7 +5,7 @@ SMRUCC.genomics.Assembly.Expasy.Database.Enzyme - + @@ -62,8 +62,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/KEGG/DBGET/BriteHEntry/BriteTerm.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/KEGG/DBGET/BriteHEntry/BriteTerm.html index ba699d8650..2450cc7afd 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/KEGG/DBGET/BriteHEntry/BriteTerm.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/KEGG/DBGET/BriteHEntry/BriteTerm.html @@ -5,7 +5,7 @@ SMRUCC.genomics.Assembly.KEGG.DBGET.BriteHEntry.BriteTerm - + @@ -60,8 +60,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/KEGG/DBGET/bGetObject/Compound.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/KEGG/DBGET/bGetObject/Compound.html index 7dd6d8d590..aae4317820 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/KEGG/DBGET/bGetObject/Compound.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/KEGG/DBGET/bGetObject/Compound.html @@ -5,7 +5,7 @@ SMRUCC.genomics.Assembly.KEGG.DBGET.bGetObject.Compound - + @@ -76,8 +76,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/KEGG/DBGET/bGetObject/OrthologyTerms.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/KEGG/DBGET/bGetObject/OrthologyTerms.html index d7f32a6533..28be3ac233 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/KEGG/DBGET/bGetObject/OrthologyTerms.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/KEGG/DBGET/bGetObject/OrthologyTerms.html @@ -5,7 +5,7 @@ SMRUCC.genomics.Assembly.KEGG.DBGET.bGetObject.OrthologyTerms - + @@ -54,8 +54,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/KEGG/DBGET/bGetObject/Reaction.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/KEGG/DBGET/bGetObject/Reaction.html index 85fbf20a8b..e8447e111f 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/KEGG/DBGET/bGetObject/Reaction.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/KEGG/DBGET/bGetObject/Reaction.html @@ -5,7 +5,7 @@ SMRUCC.genomics.Assembly.KEGG.DBGET.bGetObject.Reaction - + @@ -78,8 +78,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/KEGG/DBGET/bGetObject/ReactionClass.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/KEGG/DBGET/bGetObject/ReactionClass.html index 1396fc71c1..4dc2bd10bd 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/KEGG/DBGET/bGetObject/ReactionClass.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/KEGG/DBGET/bGetObject/ReactionClass.html @@ -5,7 +5,7 @@ SMRUCC.genomics.Assembly.KEGG.DBGET.bGetObject.ReactionClass - + @@ -69,8 +69,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/KEGG/DBGET/bGetObject/ReactionCompoundTransform.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/KEGG/DBGET/bGetObject/ReactionCompoundTransform.html index b60cd34068..7086541e48 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/KEGG/DBGET/bGetObject/ReactionCompoundTransform.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/KEGG/DBGET/bGetObject/ReactionCompoundTransform.html @@ -5,7 +5,7 @@ SMRUCC.genomics.Assembly.KEGG.DBGET.bGetObject.ReactionCompoundTransform - + @@ -50,8 +50,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/KEGG/WebServices/XML/Area.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/KEGG/WebServices/XML/Area.html index 4bf6feb2d4..8704423a74 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/KEGG/WebServices/XML/Area.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/KEGG/WebServices/XML/Area.html @@ -5,7 +5,7 @@ SMRUCC.genomics.Assembly.KEGG.WebServices.XML.Area - + @@ -69,8 +69,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/KEGG/WebServices/XML/Map.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/KEGG/WebServices/XML/Map.html index 6f2b47173b..bad16146ea 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/KEGG/WebServices/XML/Map.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/KEGG/WebServices/XML/Map.html @@ -5,7 +5,7 @@ SMRUCC.genomics.Assembly.KEGG.WebServices.XML.Map - + @@ -62,8 +62,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/KEGG/WebServices/XML/MapData.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/KEGG/WebServices/XML/MapData.html index 8a6b88311b..6e5748564a 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/KEGG/WebServices/XML/MapData.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/Assembly/KEGG/WebServices/XML/MapData.html @@ -5,7 +5,7 @@ SMRUCC.genomics.Assembly.KEGG.WebServices.XML.MapData - + @@ -53,8 +53,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/ComponentModel/Annotation/CatalogProfiles.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/ComponentModel/Annotation/CatalogProfiles.html index 81acdd96c2..dfdb33729c 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/ComponentModel/Annotation/CatalogProfiles.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/ComponentModel/Annotation/CatalogProfiles.html @@ -5,7 +5,7 @@ SMRUCC.genomics.ComponentModel.Annotation.CatalogProfiles - + @@ -53,8 +53,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/ComponentModel/Annotation/ClassProfiles.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/ComponentModel/Annotation/ClassProfiles.html index e3d5c48e35..cf02bc9b2f 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/ComponentModel/Annotation/ClassProfiles.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/ComponentModel/Annotation/ClassProfiles.html @@ -5,7 +5,7 @@ SMRUCC.genomics.ComponentModel.Annotation.ClassProfiles - + @@ -49,8 +49,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/ComponentModel/Annotation/PathwayBrief.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/ComponentModel/Annotation/PathwayBrief.html index e253109d27..646169c166 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/ComponentModel/Annotation/PathwayBrief.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/ComponentModel/Annotation/PathwayBrief.html @@ -5,7 +5,7 @@ SMRUCC.genomics.ComponentModel.Annotation.PathwayBrief - + @@ -60,8 +60,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/ComponentModel/DBLinkBuilder/DBLink.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/ComponentModel/DBLinkBuilder/DBLink.html index 2d8f029063..7bd3693f08 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/ComponentModel/DBLinkBuilder/DBLink.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/ComponentModel/DBLinkBuilder/DBLink.html @@ -5,7 +5,7 @@ SMRUCC.genomics.ComponentModel.DBLinkBuilder.DBLink - + @@ -52,8 +52,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/ComponentModel/DBLinkBuilder/Synonym.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/ComponentModel/DBLinkBuilder/Synonym.html index af6c65931b..4e04a4d8ac 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/ComponentModel/DBLinkBuilder/Synonym.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/ComponentModel/DBLinkBuilder/Synonym.html @@ -5,7 +5,7 @@ SMRUCC.genomics.ComponentModel.DBLinkBuilder.Synonym - + @@ -51,8 +51,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/ComponentModel/EquaionModel/DefaultTypes/CompoundSpecieReference.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/ComponentModel/EquaionModel/DefaultTypes/CompoundSpecieReference.html index 9357021d9a..858c4fa2ff 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/ComponentModel/EquaionModel/DefaultTypes/CompoundSpecieReference.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/ComponentModel/EquaionModel/DefaultTypes/CompoundSpecieReference.html @@ -5,7 +5,7 @@ SMRUCC.genomics.ComponentModel.EquaionModel.DefaultTypes.CompoundSpecieReference - + @@ -22,7 +22,7 @@

CompoundSpecieReference

Description

- +

the compound model reference.

Declare

@@ -50,8 +50,8 @@

.NET clr type reference tree

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.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/GCModeller/Workbench/ExperimentDesigner/SampleGroup.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/GCModeller/Workbench/ExperimentDesigner/SampleGroup.html index 3dcec3312d..dbc51bdf86 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/GCModeller/Workbench/ExperimentDesigner/SampleGroup.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/GCModeller/Workbench/ExperimentDesigner/SampleGroup.html @@ -5,7 +5,7 @@ SMRUCC.genomics.GCModeller.Workbench.ExperimentDesigner.SampleGroup - + @@ -56,8 +56,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/GCModeller/Workbench/ExperimentDesigner/SampleInfo.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/GCModeller/Workbench/ExperimentDesigner/SampleInfo.html index 4cb2d0049b..3fb352d3b2 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/GCModeller/Workbench/ExperimentDesigner/SampleInfo.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/GCModeller/Workbench/ExperimentDesigner/SampleInfo.html @@ -5,7 +5,7 @@ SMRUCC.genomics.GCModeller.Workbench.ExperimentDesigner.SampleInfo - + @@ -60,8 +60,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/GCModeller/Workbench/Knowledge_base/NCBI/MeSH/Tree/MeshCategory.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/GCModeller/Workbench/Knowledge_base/NCBI/MeSH/Tree/MeshCategory.html index f0eee0c9c7..3eac232145 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/GCModeller/Workbench/Knowledge_base/NCBI/MeSH/Tree/MeshCategory.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/GCModeller/Workbench/Knowledge_base/NCBI/MeSH/Tree/MeshCategory.html @@ -5,7 +5,7 @@ SMRUCC.genomics.GCModeller.Workbench.Knowledge_base.NCBI.MeSH.Tree.MeshCategory - + @@ -173,8 +173,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/GCModeller/Workbench/Knowledge_base/NCBI/MeSH/Tree/Term.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/GCModeller/Workbench/Knowledge_base/NCBI/MeSH/Tree/Term.html index fb0ac388e3..2d066278a5 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/GCModeller/Workbench/Knowledge_base/NCBI/MeSH/Tree/Term.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/GCModeller/Workbench/Knowledge_base/NCBI/MeSH/Tree/Term.html @@ -5,7 +5,7 @@ SMRUCC.genomics.GCModeller.Workbench.Knowledge_base.NCBI.MeSH.Tree.Term - + @@ -57,8 +57,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/foundation/OBO_Foundry/IO/Models/OBOFile.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/foundation/OBO_Foundry/IO/Models/OBOFile.html index 15c297b343..c51cf894c5 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/foundation/OBO_Foundry/IO/Models/OBOFile.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/foundation/OBO_Foundry/IO/Models/OBOFile.html @@ -5,7 +5,7 @@ SMRUCC.genomics.foundation.OBO_Foundry.IO.Models.OBOFile - + @@ -227,8 +227,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/foundation/OBO_Foundry/IO/Models/header.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/foundation/OBO_Foundry/IO/Models/header.html index f5ba94a882..cb1c3d74bf 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/foundation/OBO_Foundry/IO/Models/header.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/foundation/OBO_Foundry/IO/Models/header.html @@ -5,7 +5,7 @@ SMRUCC.genomics.foundation.OBO_Foundry.IO.Models.header - + @@ -60,8 +60,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/foundation/OBO_Foundry/Tree/GenericTree.html b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/foundation/OBO_Foundry/Tree/GenericTree.html index 9e16f69970..ff59d087bd 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/foundation/OBO_Foundry/Tree/GenericTree.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/SMRUCC/genomics/foundation/OBO_Foundry/Tree/GenericTree.html @@ -5,7 +5,7 @@ SMRUCC.genomics.foundation.OBO_Foundry.Tree.GenericTree - + @@ -59,8 +59,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Action.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Action.html index 8cde11a6c1..25cb6d80fa 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Action.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Action.html @@ -5,7 +5,7 @@ System.Action - + @@ -52,8 +52,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Array.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Array.html index d1e00e3d1c..ccb812dfc6 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Array.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Array.html @@ -5,7 +5,7 @@ System.Array - + @@ -55,8 +55,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Attribute.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Attribute.html index a88d874a77..5bffd98cb9 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Attribute.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Attribute.html @@ -5,7 +5,7 @@ System.Attribute - + @@ -49,8 +49,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Boolean.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Boolean.html index cd66d9bb41..d96fd79552 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Boolean.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Boolean.html @@ -5,7 +5,7 @@ System.Boolean - + @@ -48,8 +48,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Byte.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Byte.html index fea10fedad..0fbde71bc6 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Byte.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Byte.html @@ -5,7 +5,7 @@ System.Byte - + @@ -48,8 +48,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Collections/CollectionBase.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Collections/CollectionBase.html index 92b67c55b2..720319b937 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Collections/CollectionBase.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Collections/CollectionBase.html @@ -5,7 +5,7 @@ System.Collections.CollectionBase - + @@ -48,8 +48,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Collections/ICollection.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Collections/ICollection.html index 6b209c6729..866918a727 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Collections/ICollection.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Collections/ICollection.html @@ -5,7 +5,7 @@ System.Collections.ICollection - + @@ -51,8 +51,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Collections/IEnumerable.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Collections/IEnumerable.html index 3540e4bbdd..b0cd2fa12d 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Collections/IEnumerable.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Collections/IEnumerable.html @@ -5,7 +5,7 @@ System.Collections.IEnumerable - + @@ -46,8 +46,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Collections/Specialized/NameObjectCollectionBase+KeysCollection.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Collections/Specialized/NameObjectCollectionBase+KeysCollection.html index 726fc436e8..370a844b45 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Collections/Specialized/NameObjectCollectionBase+KeysCollection.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Collections/Specialized/NameObjectCollectionBase+KeysCollection.html @@ -5,7 +5,7 @@ System.Collections.Specialized.NameObjectCollectionBase+KeysCollection - + @@ -47,8 +47,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Collections/Specialized/NameObjectCollectionBase.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Collections/Specialized/NameObjectCollectionBase.html index 62e8aba239..72e651ab30 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Collections/Specialized/NameObjectCollectionBase.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Collections/Specialized/NameObjectCollectionBase.html @@ -5,7 +5,7 @@ System.Collections.Specialized.NameObjectCollectionBase - + @@ -50,8 +50,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Collections/Specialized/NameValueCollection.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Collections/Specialized/NameValueCollection.html index 035da843e8..b3fbb346eb 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Collections/Specialized/NameValueCollection.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Collections/Specialized/NameValueCollection.html @@ -5,7 +5,7 @@ System.Collections.Specialized.NameValueCollection - + @@ -52,8 +52,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/DateTime.html b/Rscript/Library/mzkit_app/vignettes/clr/System/DateTime.html index 1d255c5579..b4443f5e63 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/DateTime.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/DateTime.html @@ -5,7 +5,7 @@ System.DateTime - + @@ -67,8 +67,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/DateTimeKind.html b/Rscript/Library/mzkit_app/vignettes/clr/System/DateTimeKind.html index bebb4d73da..c1f5f582ee 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/DateTimeKind.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/DateTimeKind.html @@ -5,7 +5,7 @@ System.DateTimeKind - + @@ -57,8 +57,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/DayOfWeek.html b/Rscript/Library/mzkit_app/vignettes/clr/System/DayOfWeek.html index b8a53a0ea4..bdcae8688f 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/DayOfWeek.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/DayOfWeek.html @@ -5,7 +5,7 @@ System.DayOfWeek - + @@ -69,8 +69,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Decimal.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Decimal.html index 7a2eaa824f..899fcf6d31 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Decimal.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Decimal.html @@ -5,7 +5,7 @@ System.Decimal - + @@ -50,8 +50,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Delegate.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Delegate.html index 5440e3b77b..76e2709618 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Delegate.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Delegate.html @@ -5,7 +5,7 @@ System.Delegate - + @@ -51,8 +51,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Double.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Double.html index 910d7b5b5a..92df161ec5 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Double.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Double.html @@ -5,7 +5,7 @@ System.Double - + @@ -48,8 +48,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Double[].html b/Rscript/Library/mzkit_app/vignettes/clr/System/Double[].html index a45572e66b..f283f09c35 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Double[].html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Double[].html @@ -5,7 +5,7 @@ System.Double[] - + @@ -56,8 +56,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Drawing/Color.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Drawing/Color.html index c1709dcce2..15f62222a2 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Drawing/Color.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Drawing/Color.html @@ -5,7 +5,7 @@ System.Drawing.Color - + @@ -61,8 +61,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Drawing/Point.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Drawing/Point.html index 233fdd787f..18ac1ec432 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Drawing/Point.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Drawing/Point.html @@ -5,7 +5,7 @@ System.Drawing.Point - + @@ -51,8 +51,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Drawing/PointF.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Drawing/PointF.html index ede2978f0a..f10b976481 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Drawing/PointF.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Drawing/PointF.html @@ -5,7 +5,7 @@ System.Drawing.PointF - + @@ -51,8 +51,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Drawing/Rectangle.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Drawing/Rectangle.html index 1e49286b15..b4bdba9af6 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Drawing/Rectangle.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Drawing/Rectangle.html @@ -5,7 +5,7 @@ System.Drawing.Rectangle - + @@ -61,8 +61,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Drawing/RectangleF.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Drawing/RectangleF.html index 654bc26386..47ebc385ba 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Drawing/RectangleF.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Drawing/RectangleF.html @@ -5,7 +5,7 @@ System.Drawing.RectangleF - + @@ -61,8 +61,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Drawing/Size.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Drawing/Size.html index 4b5d94334e..4a16750817 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Drawing/Size.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Drawing/Size.html @@ -5,7 +5,7 @@ System.Drawing.Size - + @@ -51,8 +51,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Drawing/SizeF.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Drawing/SizeF.html index 9e88958e0c..7d1f6cc380 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Drawing/SizeF.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Drawing/SizeF.html @@ -5,7 +5,7 @@ System.Drawing.SizeF - + @@ -51,8 +51,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Enum.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Enum.html index 7ffe329d33..5dcc468e7b 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Enum.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Enum.html @@ -5,7 +5,7 @@ System.Enum - + @@ -48,8 +48,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Guid.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Guid.html index 03571f5cfa..4b2a46dc32 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Guid.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Guid.html @@ -5,7 +5,7 @@ System.Guid - + @@ -48,8 +48,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/IFormatProvider.html b/Rscript/Library/mzkit_app/vignettes/clr/System/IFormatProvider.html index 072fb6d4c7..2021c5ff82 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/IFormatProvider.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/IFormatProvider.html @@ -5,7 +5,7 @@ System.IFormatProvider - + @@ -46,8 +46,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/IO/FileAccess.html b/Rscript/Library/mzkit_app/vignettes/clr/System/IO/FileAccess.html index 7e3e785687..42aeac3404 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/IO/FileAccess.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/IO/FileAccess.html @@ -5,7 +5,7 @@ System.IO.FileAccess - + @@ -57,8 +57,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/IO/Stream.html b/Rscript/Library/mzkit_app/vignettes/clr/System/IO/Stream.html index 7298a5d432..228b758de2 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/IO/Stream.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/IO/Stream.html @@ -5,7 +5,7 @@ System.IO.Stream - + @@ -56,8 +56,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/IO/TextWriter.html b/Rscript/Library/mzkit_app/vignettes/clr/System/IO/TextWriter.html index 32e2e1a2a8..b9417d7242 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/IO/TextWriter.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/IO/TextWriter.html @@ -5,7 +5,7 @@ System.IO.TextWriter - + @@ -53,8 +53,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Int32.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Int32.html index f0e245b2a3..1e679cbabb 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Int32.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Int32.html @@ -5,7 +5,7 @@ System.Int32 - + @@ -48,8 +48,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Int64.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Int64.html index de57baeabd..96c688b51c 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Int64.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Int64.html @@ -5,7 +5,7 @@ System.Int64 - + @@ -48,8 +48,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/IntPtr.html b/Rscript/Library/mzkit_app/vignettes/clr/System/IntPtr.html index 28ceb79106..827492dff8 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/IntPtr.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/IntPtr.html @@ -5,7 +5,7 @@ System.IntPtr - + @@ -48,8 +48,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/MarshalByRefObject.html b/Rscript/Library/mzkit_app/vignettes/clr/System/MarshalByRefObject.html index eb838e99ba..41847c43b0 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/MarshalByRefObject.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/MarshalByRefObject.html @@ -5,7 +5,7 @@ System.MarshalByRefObject - + @@ -46,8 +46,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/ModuleHandle.html b/Rscript/Library/mzkit_app/vignettes/clr/System/ModuleHandle.html index a0e4b7d20c..765880906a 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/ModuleHandle.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/ModuleHandle.html @@ -5,7 +5,7 @@ System.ModuleHandle - + @@ -49,8 +49,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/MulticastDelegate.html b/Rscript/Library/mzkit_app/vignettes/clr/System/MulticastDelegate.html index 17e902d313..a568835eea 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/MulticastDelegate.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/MulticastDelegate.html @@ -5,7 +5,7 @@ System.MulticastDelegate - + @@ -52,8 +52,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Object.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Object.html index b04a66b10f..43881e2ebe 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Object.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Object.html @@ -5,7 +5,7 @@ System.Object - + @@ -46,8 +46,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/Assembly.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/Assembly.html index 74392eafe4..90320a8865 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/Assembly.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/Assembly.html @@ -5,7 +5,7 @@ System.Reflection.Assembly - + @@ -72,8 +72,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/CallingConventions.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/CallingConventions.html index 95dd86cc99..17742d8fea 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/CallingConventions.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/CallingConventions.html @@ -5,7 +5,7 @@ System.Reflection.CallingConventions - + @@ -63,8 +63,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/ConstructorInfo.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/ConstructorInfo.html index 41b46f1eff..7a311e5bc3 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/ConstructorInfo.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/ConstructorInfo.html @@ -5,7 +5,7 @@ System.Reflection.ConstructorInfo - + @@ -89,8 +89,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/CustomAttributeData.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/CustomAttributeData.html index 4c71729626..437314db7c 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/CustomAttributeData.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/CustomAttributeData.html @@ -5,7 +5,7 @@ System.Reflection.CustomAttributeData - + @@ -55,8 +55,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/CustomAttributeNamedArgument.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/CustomAttributeNamedArgument.html index 6d059f7cc9..4ee9aa4476 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/CustomAttributeNamedArgument.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/CustomAttributeNamedArgument.html @@ -5,7 +5,7 @@ System.Reflection.CustomAttributeNamedArgument - + @@ -54,8 +54,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/CustomAttributeTypedArgument.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/CustomAttributeTypedArgument.html index 94a90f7e09..8b4af49e23 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/CustomAttributeTypedArgument.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/CustomAttributeTypedArgument.html @@ -5,7 +5,7 @@ System.Reflection.CustomAttributeTypedArgument - + @@ -52,8 +52,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/EventAttributes.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/EventAttributes.html index e30343bc82..bf0c3fbecf 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/EventAttributes.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/EventAttributes.html @@ -5,7 +5,7 @@ System.Reflection.EventAttributes - + @@ -60,8 +60,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/EventInfo.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/EventInfo.html index e16bd39daa..0cc7076370 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/EventInfo.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/EventInfo.html @@ -5,7 +5,7 @@ System.Reflection.EventInfo - + @@ -73,8 +73,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/FieldAttributes.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/FieldAttributes.html index 30d822eb59..0abf2b13e4 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/FieldAttributes.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/FieldAttributes.html @@ -5,7 +5,7 @@ System.Reflection.FieldAttributes - + @@ -105,8 +105,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/FieldInfo.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/FieldInfo.html index 5b4ae8e28c..874c04af14 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/FieldInfo.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/FieldInfo.html @@ -5,7 +5,7 @@ System.Reflection.FieldInfo - + @@ -82,8 +82,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/GenericParameterAttributes.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/GenericParameterAttributes.html index 0f8ae5c9d3..27f2a8fa63 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/GenericParameterAttributes.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/GenericParameterAttributes.html @@ -5,7 +5,7 @@ System.Reflection.GenericParameterAttributes - + @@ -72,8 +72,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/ICustomAttributeProvider.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/ICustomAttributeProvider.html index de08f22724..a2842b2143 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/ICustomAttributeProvider.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/ICustomAttributeProvider.html @@ -5,7 +5,7 @@ System.Reflection.ICustomAttributeProvider - + @@ -46,8 +46,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/MemberInfo.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/MemberInfo.html index a1c917424a..18420c3525 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/MemberInfo.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/MemberInfo.html @@ -5,7 +5,7 @@ System.Reflection.MemberInfo - + @@ -60,8 +60,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/MemberTypes.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/MemberTypes.html index 4b5a033848..f5b972a18f 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/MemberTypes.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/MemberTypes.html @@ -5,7 +5,7 @@ System.Reflection.MemberTypes - + @@ -75,8 +75,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/MethodAttributes.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/MethodAttributes.html index ecd96ac415..d42266562f 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/MethodAttributes.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/MethodAttributes.html @@ -5,7 +5,7 @@ System.Reflection.MethodAttributes - + @@ -120,8 +120,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/MethodBase.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/MethodBase.html index 392acdc7a6..7e9e623afa 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/MethodBase.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/MethodBase.html @@ -5,7 +5,7 @@ System.Reflection.MethodBase - + @@ -89,8 +89,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/MethodImplAttributes.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/MethodImplAttributes.html index 9c104b4fd3..3adba53813 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/MethodImplAttributes.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/MethodImplAttributes.html @@ -5,7 +5,7 @@ System.Reflection.MethodImplAttributes - + @@ -99,8 +99,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/MethodInfo.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/MethodInfo.html index b0dbc0014b..ca89a7cc53 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/MethodInfo.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/MethodInfo.html @@ -5,7 +5,7 @@ System.Reflection.MethodInfo - + @@ -95,8 +95,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/Module.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/Module.html index 11d2b976d2..09c6cb1678 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/Module.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/Module.html @@ -5,7 +5,7 @@ System.Reflection.Module - + @@ -60,8 +60,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/ParameterAttributes.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/ParameterAttributes.html index c52d216c23..fff79d28c9 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/ParameterAttributes.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/ParameterAttributes.html @@ -5,7 +5,7 @@ System.Reflection.ParameterAttributes - + @@ -81,8 +81,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/ParameterInfo.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/ParameterInfo.html index 47b5b015dc..ea619d28fa 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/ParameterInfo.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/ParameterInfo.html @@ -5,7 +5,7 @@ System.Reflection.ParameterInfo - + @@ -68,8 +68,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/PropertyAttributes.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/PropertyAttributes.html index a346ee4953..73c2dcc5de 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/PropertyAttributes.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/PropertyAttributes.html @@ -5,7 +5,7 @@ System.Reflection.PropertyAttributes - + @@ -72,8 +72,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/PropertyInfo.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/PropertyInfo.html index bae9891898..85cfb828a8 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/PropertyInfo.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/PropertyInfo.html @@ -5,7 +5,7 @@ System.Reflection.PropertyInfo - + @@ -72,8 +72,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/TypeAttributes.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/TypeAttributes.html index e50882ff28..6b176a59a9 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/TypeAttributes.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/TypeAttributes.html @@ -5,7 +5,7 @@ System.Reflection.TypeAttributes - + @@ -144,8 +144,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/TypeInfo.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/TypeInfo.html index acb4e5178b..792dfc156e 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/TypeInfo.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Reflection/TypeInfo.html @@ -5,7 +5,7 @@ System.Reflection.TypeInfo - + @@ -155,8 +155,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Runtime/InteropServices/LayoutKind.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Runtime/InteropServices/LayoutKind.html index f863f9723e..01642634c4 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Runtime/InteropServices/LayoutKind.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Runtime/InteropServices/LayoutKind.html @@ -5,7 +5,7 @@ System.Runtime.InteropServices.LayoutKind - + @@ -57,8 +57,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Runtime/InteropServices/StructLayoutAttribute.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Runtime/InteropServices/StructLayoutAttribute.html index 7bb9c22e47..cb22149dfa 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Runtime/InteropServices/StructLayoutAttribute.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Runtime/InteropServices/StructLayoutAttribute.html @@ -5,7 +5,7 @@ System.Runtime.InteropServices.StructLayoutAttribute - + @@ -52,8 +52,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/RuntimeFieldHandle.html b/Rscript/Library/mzkit_app/vignettes/clr/System/RuntimeFieldHandle.html index 8a052cec5a..17f371d0d4 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/RuntimeFieldHandle.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/RuntimeFieldHandle.html @@ -5,7 +5,7 @@ System.RuntimeFieldHandle - + @@ -50,8 +50,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/RuntimeMethodHandle.html b/Rscript/Library/mzkit_app/vignettes/clr/System/RuntimeMethodHandle.html index d5932fe4b2..8b8d284692 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/RuntimeMethodHandle.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/RuntimeMethodHandle.html @@ -5,7 +5,7 @@ System.RuntimeMethodHandle - + @@ -50,8 +50,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/RuntimeTypeHandle.html b/Rscript/Library/mzkit_app/vignettes/clr/System/RuntimeTypeHandle.html index 0721302fe9..4388bb2ffc 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/RuntimeTypeHandle.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/RuntimeTypeHandle.html @@ -5,7 +5,7 @@ System.RuntimeTypeHandle - + @@ -50,8 +50,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/SByte.html b/Rscript/Library/mzkit_app/vignettes/clr/System/SByte.html index 93775b3073..7bf32b55ca 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/SByte.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/SByte.html @@ -5,7 +5,7 @@ System.SByte - + @@ -48,8 +48,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Security/SecurityRuleSet.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Security/SecurityRuleSet.html index 1174a5f3f2..e84ca142dc 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Security/SecurityRuleSet.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Security/SecurityRuleSet.html @@ -5,7 +5,7 @@ System.Security.SecurityRuleSet - + @@ -57,8 +57,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Single.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Single.html index 6745feedbb..8f67ab5bd4 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Single.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Single.html @@ -5,7 +5,7 @@ System.Single - + @@ -48,8 +48,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/String.html b/Rscript/Library/mzkit_app/vignettes/clr/System/String.html index 52d32ccb4c..d9b3616dbd 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/String.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/String.html @@ -5,7 +5,7 @@ System.String - + @@ -47,8 +47,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Text/DecoderFallback.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Text/DecoderFallback.html index c1a98b28fa..69a4c8372e 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Text/DecoderFallback.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Text/DecoderFallback.html @@ -5,7 +5,7 @@ System.Text.DecoderFallback - + @@ -47,8 +47,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Text/EncoderFallback.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Text/EncoderFallback.html index 49535a5200..8309eac615 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Text/EncoderFallback.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Text/EncoderFallback.html @@ -5,7 +5,7 @@ System.Text.EncoderFallback - + @@ -47,8 +47,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Text/Encoding.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Text/Encoding.html index e37ab85f43..b2af5b9d10 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Text/Encoding.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Text/Encoding.html @@ -5,7 +5,7 @@ System.Text.Encoding - + @@ -65,8 +65,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/TimeSpan.html b/Rscript/Library/mzkit_app/vignettes/clr/System/TimeSpan.html index 1ee1201549..29d7f7aeb4 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/TimeSpan.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/TimeSpan.html @@ -5,7 +5,7 @@ System.TimeSpan - + @@ -63,8 +63,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Type.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Type.html index f04b684eb5..6d8c5fa923 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Type.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Type.html @@ -5,7 +5,7 @@ System.Type - + @@ -137,8 +137,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/ValueType.html b/Rscript/Library/mzkit_app/vignettes/clr/System/ValueType.html index 2b67e31cac..d326d648e1 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/ValueType.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/ValueType.html @@ -5,7 +5,7 @@ System.ValueType - + @@ -46,8 +46,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/IXmlSchemaInfo.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/IXmlSchemaInfo.html index 101174e6c6..f06237ff8f 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/IXmlSchemaInfo.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/IXmlSchemaInfo.html @@ -5,7 +5,7 @@ System.Xml.Schema.IXmlSchemaInfo - + @@ -59,8 +59,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaAnnotated.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaAnnotated.html index 8914d0738f..97461dd74a 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaAnnotated.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaAnnotated.html @@ -5,7 +5,7 @@ System.Xml.Schema.XmlSchemaAnnotated - + @@ -60,8 +60,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaAnnotation.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaAnnotation.html index c37719ef50..81e1e633d1 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaAnnotation.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaAnnotation.html @@ -5,7 +5,7 @@ System.Xml.Schema.XmlSchemaAnnotation - + @@ -60,8 +60,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaAttribute.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaAttribute.html index 970bb6c8a7..f87d03faf9 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaAttribute.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaAttribute.html @@ -5,7 +5,7 @@ System.Xml.Schema.XmlSchemaAttribute - + @@ -79,8 +79,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaCompilationSettings.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaCompilationSettings.html index 5e3ce37685..55e9cb7834 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaCompilationSettings.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaCompilationSettings.html @@ -5,7 +5,7 @@ System.Xml.Schema.XmlSchemaCompilationSettings - + @@ -47,8 +47,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaDatatype.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaDatatype.html index 74630f6ed3..3df22038fe 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaDatatype.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaDatatype.html @@ -5,7 +5,7 @@ System.Xml.Schema.XmlSchemaDatatype - + @@ -55,8 +55,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaDatatypeVariety.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaDatatypeVariety.html index 3bf8bb39b6..2bcc82de68 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaDatatypeVariety.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaDatatypeVariety.html @@ -5,7 +5,7 @@ System.Xml.Schema.XmlSchemaDatatypeVariety - + @@ -57,8 +57,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaDerivationMethod.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaDerivationMethod.html index a140712205..851ed636b6 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaDerivationMethod.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaDerivationMethod.html @@ -5,7 +5,7 @@ System.Xml.Schema.XmlSchemaDerivationMethod - + @@ -72,8 +72,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaElement.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaElement.html index 3cc070c208..5d33e5b0bc 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaElement.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaElement.html @@ -5,7 +5,7 @@ System.Xml.Schema.XmlSchemaElement - + @@ -97,8 +97,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaForm.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaForm.html index d8146f99ee..ece52e11e7 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaForm.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaForm.html @@ -5,7 +5,7 @@ System.Xml.Schema.XmlSchemaForm - + @@ -57,8 +57,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaObject.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaObject.html index 4884a61bd2..d0e054328f 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaObject.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaObject.html @@ -5,7 +5,7 @@ System.Xml.Schema.XmlSchemaObject - + @@ -54,8 +54,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaObjectCollection.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaObjectCollection.html index 6c0c2782db..a763c421ad 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaObjectCollection.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaObjectCollection.html @@ -5,7 +5,7 @@ System.Xml.Schema.XmlSchemaObjectCollection - + @@ -50,8 +50,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaObjectTable.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaObjectTable.html index 56110bbca4..6fbe533cda 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaObjectTable.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaObjectTable.html @@ -5,7 +5,7 @@ System.Xml.Schema.XmlSchemaObjectTable - + @@ -52,8 +52,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaParticle.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaParticle.html index ff58b28177..d7ef2335b8 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaParticle.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaParticle.html @@ -5,7 +5,7 @@ System.Xml.Schema.XmlSchemaParticle - + @@ -66,8 +66,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaSet.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaSet.html index 2afe563681..38d09a8fa2 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaSet.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaSet.html @@ -5,7 +5,7 @@ System.Xml.Schema.XmlSchemaSet - + @@ -59,8 +59,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaSimpleType.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaSimpleType.html index 8833fac517..40ddc734e2 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaSimpleType.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaSimpleType.html @@ -5,7 +5,7 @@ System.Xml.Schema.XmlSchemaSimpleType - + @@ -80,8 +80,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaSimpleTypeContent.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaSimpleTypeContent.html index 7457f75fb1..9c178accd1 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaSimpleTypeContent.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaSimpleTypeContent.html @@ -5,7 +5,7 @@ System.Xml.Schema.XmlSchemaSimpleTypeContent - + @@ -60,8 +60,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaType.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaType.html index e131e72a78..8b94ce669b 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaType.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaType.html @@ -5,7 +5,7 @@ System.Xml.Schema.XmlSchemaType - + @@ -78,8 +78,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaUse.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaUse.html index 3c9b1bda6d..506e85c7b8 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaUse.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaUse.html @@ -5,7 +5,7 @@ System.Xml.Schema.XmlSchemaUse - + @@ -60,8 +60,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaValidity.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaValidity.html index 3cc4f7de49..35d3d23e8f 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaValidity.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlSchemaValidity.html @@ -5,7 +5,7 @@ System.Xml.Schema.XmlSchemaValidity - + @@ -57,8 +57,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlTypeCode.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlTypeCode.html index f413e3bbe8..2ee9e3e679 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlTypeCode.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Schema/XmlTypeCode.html @@ -5,7 +5,7 @@ System.Xml.Schema.XmlTypeCode - + @@ -213,8 +213,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Serialization/XmlSerializerNamespaces.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Serialization/XmlSerializerNamespaces.html index bb8d6e4aac..a6cebdc40a 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Serialization/XmlSerializerNamespaces.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/Serialization/XmlSerializerNamespaces.html @@ -5,7 +5,7 @@ System.Xml.Serialization.XmlSerializerNamespaces - + @@ -47,8 +47,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlAttribute.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlAttribute.html index f507d6f2b6..9d603769af 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlAttribute.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlAttribute.html @@ -5,7 +5,7 @@ System.Xml.XmlAttribute - + @@ -82,8 +82,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlAttributeCollection.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlAttributeCollection.html index 8e5a47cbc4..fcd7a2d042 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlAttributeCollection.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlAttributeCollection.html @@ -5,7 +5,7 @@ System.Xml.XmlAttributeCollection - + @@ -49,8 +49,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlCharacterData.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlCharacterData.html index ef806afa11..a8c54c3fa4 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlCharacterData.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlCharacterData.html @@ -5,7 +5,7 @@ System.Xml.XmlCharacterData - + @@ -83,8 +83,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlComment.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlComment.html index 3917d77221..b75f9da365 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlComment.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlComment.html @@ -5,7 +5,7 @@ System.Xml.XmlComment - + @@ -83,8 +83,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlDocument.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlDocument.html index 8841c7d38c..83722cb0ea 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlDocument.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlDocument.html @@ -5,7 +5,7 @@ System.Xml.XmlDocument - + @@ -91,8 +91,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlDocumentType.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlDocumentType.html index 308781d8f8..c09c5f21e1 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlDocumentType.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlDocumentType.html @@ -5,7 +5,7 @@ System.Xml.XmlDocumentType - + @@ -88,8 +88,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlElement.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlElement.html index 24fa203f38..caabc2ccd8 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlElement.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlElement.html @@ -5,7 +5,7 @@ System.Xml.XmlElement - + @@ -83,8 +83,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlImplementation.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlImplementation.html index c4be00d579..81f18cd0b2 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlImplementation.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlImplementation.html @@ -5,7 +5,7 @@ System.Xml.XmlImplementation - + @@ -46,8 +46,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlLinkedNode.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlLinkedNode.html index 657be27c5f..6488f8c17d 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlLinkedNode.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlLinkedNode.html @@ -5,7 +5,7 @@ System.Xml.XmlLinkedNode - + @@ -81,8 +81,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlNameTable.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlNameTable.html index a0e761c87d..f4c4a6891a 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlNameTable.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlNameTable.html @@ -5,7 +5,7 @@ System.Xml.XmlNameTable - + @@ -46,8 +46,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlNamedNodeMap.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlNamedNodeMap.html index 4169361c8d..777b624585 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlNamedNodeMap.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlNamedNodeMap.html @@ -5,7 +5,7 @@ System.Xml.XmlNamedNodeMap - + @@ -47,8 +47,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlNode.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlNode.html index 47dec516fc..9ed32e8006 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlNode.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlNode.html @@ -5,7 +5,7 @@ System.Xml.XmlNode - + @@ -80,8 +80,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlNodeList.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlNodeList.html index d0dd6e24af..2569512ce2 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlNodeList.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlNodeList.html @@ -5,7 +5,7 @@ System.Xml.XmlNodeList - + @@ -47,8 +47,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlNodeType.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlNodeType.html index 06d068a587..5aa958d7c0 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlNodeType.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlNodeType.html @@ -5,7 +5,7 @@ System.Xml.XmlNodeType - + @@ -102,8 +102,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlQualifiedName.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlQualifiedName.html index e6be9fa655..6b12f3c4a9 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlQualifiedName.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlQualifiedName.html @@ -5,7 +5,7 @@ System.Xml.XmlQualifiedName - + @@ -49,8 +49,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlTokenizedType.html b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlTokenizedType.html index 02ddc8437a..d6878821db 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlTokenizedType.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/System/Xml/XmlTokenizedType.html @@ -5,7 +5,7 @@ System.Xml.XmlTokenizedType - + @@ -87,8 +87,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/mzkit/LinearDataSet.html b/Rscript/Library/mzkit_app/vignettes/clr/mzkit/LinearDataSet.html index bc9b2c1387..eb593db4f6 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/mzkit/LinearDataSet.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/mzkit/LinearDataSet.html @@ -5,7 +5,7 @@ mzkit.LinearDataSet - + @@ -46,8 +46,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/clr/mzkit/QCData.html b/Rscript/Library/mzkit_app/vignettes/clr/mzkit/QCData.html index 2cf7a66da9..0b70c897dd 100644 --- a/Rscript/Library/mzkit_app/vignettes/clr/mzkit/QCData.html +++ b/Rscript/Library/mzkit_app/vignettes/clr/mzkit/QCData.html @@ -5,7 +5,7 @@ mzkit.QCData - + @@ -52,8 +52,8 @@

.NET clr type reference tree

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzDIA/DIA/dia_nmf.html b/Rscript/Library/mzkit_app/vignettes/mzDIA/DIA/dia_nmf.html index 1545de9692..6048239b9a 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzDIA/DIA/dia_nmf.html +++ b/Rscript/Library/mzkit_app/vignettes/mzDIA/DIA/dia_nmf.html @@ -5,7 +5,7 @@ make the spectrum set decompose into multiple spectrum groups via the NMF method - + @@ -76,8 +76,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzDIA/MoleculeNetworking/as.graph.html b/Rscript/Library/mzkit_app/vignettes/mzDIA/MoleculeNetworking/as.graph.html index b8e07b138d..9d0fad1431 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzDIA/MoleculeNetworking/as.graph.html +++ b/Rscript/Library/mzkit_app/vignettes/mzDIA/MoleculeNetworking/as.graph.html @@ -5,7 +5,7 @@ convert the cluster tree into the graph model - + @@ -67,8 +67,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzDIA/MoleculeNetworking/clustering.html b/Rscript/Library/mzkit_app/vignettes/mzDIA/MoleculeNetworking/clustering.html index c4f751ea4c..679834dd60 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzDIA/MoleculeNetworking/clustering.html +++ b/Rscript/Library/mzkit_app/vignettes/mzDIA/MoleculeNetworking/clustering.html @@ -5,7 +5,7 @@ Do spectrum clustering on a small bundle of the ms2 spectrum from a single raw data file - + @@ -101,8 +101,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzDIA/MoleculeNetworking/grid_assigned.html b/Rscript/Library/mzkit_app/vignettes/mzDIA/MoleculeNetworking/grid_assigned.html index 254c92a07e..a694e760d3 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzDIA/MoleculeNetworking/grid_assigned.html +++ b/Rscript/Library/mzkit_app/vignettes/mzDIA/MoleculeNetworking/grid_assigned.html @@ -5,7 +5,7 @@ Make precursor assigned to the cluster node - + @@ -68,8 +68,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzDIA/MoleculeNetworking/msBin.html b/Rscript/Library/mzkit_app/vignettes/mzDIA/MoleculeNetworking/msBin.html index f4c82afb53..d0c7f6ab82 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzDIA/MoleculeNetworking/msBin.html +++ b/Rscript/Library/mzkit_app/vignettes/mzDIA/MoleculeNetworking/msBin.html @@ -5,7 +5,7 @@ populate a list of peak ms2 cluster data - + @@ -67,8 +67,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzDIA/MoleculeNetworking/representative.html b/Rscript/Library/mzkit_app/vignettes/mzDIA/MoleculeNetworking/representative.html index 1583d54662..e16e7d71ea 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzDIA/MoleculeNetworking/representative.html +++ b/Rscript/Library/mzkit_app/vignettes/mzDIA/MoleculeNetworking/representative.html @@ -5,7 +5,7 @@ create representative spectrum data - + @@ -68,8 +68,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzDIA/MoleculeNetworking/spectrum_clusters.html b/Rscript/Library/mzkit_app/vignettes/mzDIA/MoleculeNetworking/spectrum_clusters.html index 819090ddf9..a2afce9a0f 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzDIA/MoleculeNetworking/spectrum_clusters.html +++ b/Rscript/Library/mzkit_app/vignettes/mzDIA/MoleculeNetworking/spectrum_clusters.html @@ -5,7 +5,7 @@ get all aligned spectrum clusters across rawdata files - + @@ -63,8 +63,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzDIA/MoleculeNetworking/spectrum_grid.html b/Rscript/Library/mzkit_app/vignettes/mzDIA/MoleculeNetworking/spectrum_grid.html index 58d3ec4465..c48d268723 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzDIA/MoleculeNetworking/spectrum_grid.html +++ b/Rscript/Library/mzkit_app/vignettes/mzDIA/MoleculeNetworking/spectrum_grid.html @@ -5,7 +5,7 @@ Create grid clustering of the ms2 spectrum data - + @@ -86,8 +86,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzDIA/MoleculeNetworking/splitClusterRT.html b/Rscript/Library/mzkit_app/vignettes/mzDIA/MoleculeNetworking/splitClusterRT.html index 08e0709017..e2b8941789 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzDIA/MoleculeNetworking/splitClusterRT.html +++ b/Rscript/Library/mzkit_app/vignettes/mzDIA/MoleculeNetworking/splitClusterRT.html @@ -5,7 +5,7 @@ Split each cluster data into multiple parts by a givne rt window - + @@ -82,8 +82,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzDIA/MoleculeNetworking/tree.html b/Rscript/Library/mzkit_app/vignettes/mzDIA/MoleculeNetworking/tree.html index 4040ae24a9..6935745e84 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzDIA/MoleculeNetworking/tree.html +++ b/Rscript/Library/mzkit_app/vignettes/mzDIA/MoleculeNetworking/tree.html @@ -5,7 +5,7 @@ do spectrum data clustering - + @@ -80,8 +80,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzDIA/MoleculeNetworking/uniqueNames.html b/Rscript/Library/mzkit_app/vignettes/mzDIA/MoleculeNetworking/uniqueNames.html index fbf6144d55..12775ade0b 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzDIA/MoleculeNetworking/uniqueNames.html +++ b/Rscript/Library/mzkit_app/vignettes/mzDIA/MoleculeNetworking/uniqueNames.html @@ -5,7 +5,7 @@ makes the spectrum data its unique id reference uniqued! - + @@ -63,8 +63,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzDIA/MoleculeNetworking/unpack_assign.html b/Rscript/Library/mzkit_app/vignettes/mzDIA/MoleculeNetworking/unpack_assign.html index 9f55da8b31..30fd9defff 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzDIA/MoleculeNetworking/unpack_assign.html +++ b/Rscript/Library/mzkit_app/vignettes/mzDIA/MoleculeNetworking/unpack_assign.html @@ -5,7 +5,7 @@ Unpack of the spectrum data into multiple file groups - + @@ -68,8 +68,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzDIA/MoleculeNetworking/unpack_unmapped.html b/Rscript/Library/mzkit_app/vignettes/mzDIA/MoleculeNetworking/unpack_unmapped.html index 95002185d8..cab2e82ecd 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzDIA/MoleculeNetworking/unpack_unmapped.html +++ b/Rscript/Library/mzkit_app/vignettes/mzDIA/MoleculeNetworking/unpack_unmapped.html @@ -5,7 +5,7 @@ unpack_unmapped - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzDIA/Oligonucleotide_MS/exact_mass.html b/Rscript/Library/mzkit_app/vignettes/mzDIA/Oligonucleotide_MS/exact_mass.html index 171c19adfb..a50d4457d3 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzDIA/Oligonucleotide_MS/exact_mass.html +++ b/Rscript/Library/mzkit_app/vignettes/mzDIA/Oligonucleotide_MS/exact_mass.html @@ -5,7 +5,7 @@ evaluate the exact mass for the gene sequence - + @@ -63,8 +63,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzDIA/lipidomics/adduct.html b/Rscript/Library/mzkit_app/vignettes/mzDIA/lipidomics/adduct.html index a26964f151..cc923ebd9f 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzDIA/lipidomics/adduct.html +++ b/Rscript/Library/mzkit_app/vignettes/mzDIA/lipidomics/adduct.html @@ -5,7 +5,7 @@ create the adduct ion data model - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzDIA/lipidomics/lipid_ions.html b/Rscript/Library/mzkit_app/vignettes/mzDIA/lipidomics/lipid_ions.html index fa1d546dec..205b13693c 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzDIA/lipidomics/lipid_ions.html +++ b/Rscript/Library/mzkit_app/vignettes/mzDIA/lipidomics/lipid_ions.html @@ -5,7 +5,7 @@ meansrue lipid ions - + @@ -87,8 +87,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzDIA/lipidomics/lipidmaps.html b/Rscript/Library/mzkit_app/vignettes/mzDIA/lipidomics/lipidmaps.html index 10a699aee0..99df260e60 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzDIA/lipidomics/lipidmaps.html +++ b/Rscript/Library/mzkit_app/vignettes/mzDIA/lipidomics/lipidmaps.html @@ -5,7 +5,7 @@ create a lipidmaps metabolite data indexer - + @@ -67,8 +67,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzDIA/lipidomics/mapping.html b/Rscript/Library/mzkit_app/vignettes/mzDIA/lipidomics/mapping.html index 3559fa7f11..911a072487 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzDIA/lipidomics/mapping.html +++ b/Rscript/Library/mzkit_app/vignettes/mzDIA/lipidomics/mapping.html @@ -5,7 +5,7 @@ get mapping of the lipidmaps reference id via lipid name - + @@ -71,8 +71,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/DIA.infer.html b/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/DIA.infer.html index 50b6c2dcad..a75185a463 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/DIA.infer.html +++ b/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/DIA.infer.html @@ -5,7 +5,7 @@ apply of the metadna annotation workflow - + @@ -77,8 +77,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/annotationSet.html b/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/annotationSet.html index 8cf98983b0..6348ea1dd6 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/annotationSet.html +++ b/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/annotationSet.html @@ -5,7 +5,7 @@ Create the kegg compound ms1 annotation query engine. - + @@ -84,8 +84,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/as.graph.html b/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/as.graph.html index 444ec7b062..c69dd1bebb 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/as.graph.html +++ b/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/as.graph.html @@ -5,7 +5,7 @@ as.graph - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/as.seeds.html b/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/as.seeds.html index 50b8f89542..db5ed3e413 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/as.seeds.html +++ b/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/as.seeds.html @@ -5,7 +5,7 @@ create seeds from mgf file data - + @@ -68,8 +68,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/as.table.html b/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/as.table.html index 439f19819c..1723bc9c7f 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/as.table.html +++ b/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/as.table.html @@ -5,7 +5,7 @@ Extract the annotation result from metaDNA algorithm module as data table - + @@ -82,8 +82,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/as.ticks.html b/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/as.ticks.html index 20bd67e115..8c4f0614c2 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/as.ticks.html +++ b/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/as.ticks.html @@ -5,7 +5,7 @@ as.ticks - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/kegg.library.html b/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/kegg.library.html index 33bd4d8d54..2891f9ac5c 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/kegg.library.html +++ b/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/kegg.library.html @@ -5,7 +5,7 @@ load kegg compounds - + @@ -63,8 +63,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/kegg.network.html b/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/kegg.network.html index f284d20e8e..b000608516 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/kegg.network.html +++ b/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/kegg.network.html @@ -5,7 +5,7 @@ load the kegg reaction class data. - + @@ -63,8 +63,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/load.kegg.html b/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/load.kegg.html index 42468abcec..e266948d1a 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/load.kegg.html +++ b/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/load.kegg.html @@ -5,7 +5,7 @@ Set kegg compound library - + @@ -72,8 +72,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/load.kegg_network.html b/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/load.kegg_network.html index fab2bfe08b..fdabcf8529 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/load.kegg_network.html +++ b/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/load.kegg_network.html @@ -5,7 +5,7 @@ set the kegg reaction class data links for the compounds - + @@ -71,8 +71,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/load.ontology.html b/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/load.ontology.html index 94217212fb..7433d7e191 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/load.ontology.html +++ b/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/load.ontology.html @@ -5,7 +5,7 @@ load the ontology tree as the network graph for search - + @@ -71,8 +71,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/load.raw.html b/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/load.raw.html index 1b7fbf6c88..261505ff6a 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/load.raw.html +++ b/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/load.raw.html @@ -5,7 +5,7 @@ set ms2 spectrum data for run the annotation - + @@ -78,8 +78,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/metadna.html b/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/metadna.html index e64bbd46e5..aa5d7dde95 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/metadna.html +++ b/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/metadna.html @@ -5,7 +5,7 @@ Create an algorithm module for run metaDNA inferance - + @@ -89,8 +89,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/range.html b/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/range.html index 42559d811c..d72c7c4d24 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/range.html +++ b/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/range.html @@ -5,7 +5,7 @@ Configs the precursor adducts range for the metaDNA algorithm - + @@ -72,8 +72,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/reaction_class.table.html b/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/reaction_class.table.html index 6fa6140c31..5df382e9c4 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/reaction_class.table.html +++ b/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/reaction_class.table.html @@ -5,7 +5,7 @@ load kegg reaction class data in table format from given file - + @@ -68,8 +68,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/read.infer_details.html b/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/read.infer_details.html index a49028beb9..586f173c09 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/read.infer_details.html +++ b/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/read.infer_details.html @@ -5,7 +5,7 @@ read.infer_details - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/read.metadna.infer.html b/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/read.metadna.infer.html index 9cfb8f944a..48a50c3251 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/read.metadna.infer.html +++ b/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/read.metadna.infer.html @@ -5,7 +5,7 @@ Load network graph model from the kegg metaDNA infer network data. - + @@ -67,8 +67,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/result.alignment.html b/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/result.alignment.html index 9ce87899da..13a94db4dd 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/result.alignment.html +++ b/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/result.alignment.html @@ -5,7 +5,7 @@ get result alignments raw data for data plots. - + @@ -71,8 +71,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/setLibrary.html b/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/setLibrary.html index 2368ea4f71..9b865ab340 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/setLibrary.html +++ b/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/setLibrary.html @@ -5,7 +5,7 @@ - + @@ -71,8 +71,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/setNetworking.html b/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/setNetworking.html index 940d81c60b..1b0ff75f3a 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/setNetworking.html +++ b/Rscript/Library/mzkit_app/vignettes/mzDIA/metadna/setNetworking.html @@ -5,7 +5,7 @@ - + @@ -67,8 +67,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzDIA/spectral_simulator/buildDocuments.html b/Rscript/Library/mzkit_app/vignettes/mzDIA/spectral_simulator/buildDocuments.html index 8a806c68ea..4e62a0508e 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzDIA/spectral_simulator/buildDocuments.html +++ b/Rscript/Library/mzkit_app/vignettes/mzDIA/spectral_simulator/buildDocuments.html @@ -5,7 +5,7 @@ build molecule documents for do embedding - + @@ -64,8 +64,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzDIA/spectral_simulator/embedded.graph2vector.html b/Rscript/Library/mzkit_app/vignettes/mzDIA/spectral_simulator/embedded.graph2vector.html index 8b3b7df693..4715f282fe 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzDIA/spectral_simulator/embedded.graph2vector.html +++ b/Rscript/Library/mzkit_app/vignettes/mzDIA/spectral_simulator/embedded.graph2vector.html @@ -5,7 +5,7 @@ make the molecular graph embedding to vector - + @@ -67,8 +67,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzDIA/spectral_simulator/molecular_graph.html b/Rscript/Library/mzkit_app/vignettes/mzDIA/spectral_simulator/molecular_graph.html index c208b4d51f..2cb7f01f05 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzDIA/spectral_simulator/molecular_graph.html +++ b/Rscript/Library/mzkit_app/vignettes/mzDIA/spectral_simulator/molecular_graph.html @@ -5,7 +5,7 @@ parse the smiles structure string as molecular network graph - + @@ -77,8 +77,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzDIA/spectral_simulator/read.kcf.html b/Rscript/Library/mzkit_app/vignettes/mzDIA/spectral_simulator/read.kcf.html index afec7e2fbd..f06eeebcbb 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzDIA/spectral_simulator/read.kcf.html +++ b/Rscript/Library/mzkit_app/vignettes/mzDIA/spectral_simulator/read.kcf.html @@ -5,7 +5,7 @@ read.kcf - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzDIA/spectrumPool/addPool.html b/Rscript/Library/mzkit_app/vignettes/mzDIA/spectrumPool/addPool.html index 0be7d25b1c..48ca87f491 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzDIA/spectrumPool/addPool.html +++ b/Rscript/Library/mzkit_app/vignettes/mzDIA/spectrumPool/addPool.html @@ -5,7 +5,7 @@ add sample peaks data to spectrum pool - + @@ -86,8 +86,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzDIA/spectrumPool/closePool.html b/Rscript/Library/mzkit_app/vignettes/mzDIA/spectrumPool/closePool.html index b3f0feabc3..80012f97ca 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzDIA/spectrumPool/closePool.html +++ b/Rscript/Library/mzkit_app/vignettes/mzDIA/spectrumPool/closePool.html @@ -5,7 +5,7 @@ close the connection to the spectrum pool - + @@ -64,8 +64,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzDIA/spectrumPool/commit.html b/Rscript/Library/mzkit_app/vignettes/mzDIA/spectrumPool/commit.html index 88e769cbff..7968ce1383 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzDIA/spectrumPool/commit.html +++ b/Rscript/Library/mzkit_app/vignettes/mzDIA/spectrumPool/commit.html @@ -5,7 +5,7 @@ commit data to the spectrum pool database - + @@ -64,8 +64,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzDIA/spectrumPool/conservedGuid.html b/Rscript/Library/mzkit_app/vignettes/mzDIA/spectrumPool/conservedGuid.html index 5d9a037e11..f5adfab966 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzDIA/spectrumPool/conservedGuid.html +++ b/Rscript/Library/mzkit_app/vignettes/mzDIA/spectrumPool/conservedGuid.html @@ -5,7 +5,7 @@ generates the guid for the spectrum with unknown annotation - + @@ -71,8 +71,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzDIA/spectrumPool/createPool.html b/Rscript/Library/mzkit_app/vignettes/mzDIA/spectrumPool/createPool.html index 94c75f1828..cc52273be0 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzDIA/spectrumPool/createPool.html +++ b/Rscript/Library/mzkit_app/vignettes/mzDIA/spectrumPool/createPool.html @@ -5,7 +5,7 @@ create a new spectrum clustering data pool - + @@ -75,8 +75,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzDIA/spectrumPool/getClusterInfo.html b/Rscript/Library/mzkit_app/vignettes/mzDIA/spectrumPool/getClusterInfo.html index d1619682d3..7c88217c07 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzDIA/spectrumPool/getClusterInfo.html +++ b/Rscript/Library/mzkit_app/vignettes/mzDIA/spectrumPool/getClusterInfo.html @@ -5,7 +5,7 @@ get metadata dataframe in a given cluster tree - + @@ -82,8 +82,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzDIA/spectrumPool/infer.html b/Rscript/Library/mzkit_app/vignettes/mzDIA/spectrumPool/infer.html index 3c7713b8e2..a10cf49fcf 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzDIA/spectrumPool/infer.html +++ b/Rscript/Library/mzkit_app/vignettes/mzDIA/spectrumPool/infer.html @@ -5,7 +5,7 @@ Infer and make annotation to a specific cluster - + @@ -79,8 +79,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzDIA/spectrumPool/load_infer.html b/Rscript/Library/mzkit_app/vignettes/mzDIA/spectrumPool/load_infer.html index 0128ec37b4..51b7bc3768 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzDIA/spectrumPool/load_infer.html +++ b/Rscript/Library/mzkit_app/vignettes/mzDIA/spectrumPool/load_infer.html @@ -5,7 +5,7 @@ Create a spectrum inference protocol workflow - + @@ -70,8 +70,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzDIA/spectrumPool/model_id.html b/Rscript/Library/mzkit_app/vignettes/mzDIA/spectrumPool/model_id.html index d49f80e5ac..702b94cdd8 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzDIA/spectrumPool/model_id.html +++ b/Rscript/Library/mzkit_app/vignettes/mzDIA/spectrumPool/model_id.html @@ -5,7 +5,7 @@ get model id from the spectrum cluster graph model - + @@ -63,8 +63,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzDIA/spectrumPool/openPool.html b/Rscript/Library/mzkit_app/vignettes/mzDIA/spectrumPool/openPool.html index 3ff9ec9495..ed8ad6286d 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzDIA/spectrumPool/openPool.html +++ b/Rscript/Library/mzkit_app/vignettes/mzDIA/spectrumPool/openPool.html @@ -5,7 +5,7 @@ open the spectrum pool from a given resource link - + @@ -77,8 +77,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzDIA/spectrumPool/set_conservedGuid.html b/Rscript/Library/mzkit_app/vignettes/mzDIA/spectrumPool/set_conservedGuid.html index 2453feec54..a1efaa53ee 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzDIA/spectrumPool/set_conservedGuid.html +++ b/Rscript/Library/mzkit_app/vignettes/mzDIA/spectrumPool/set_conservedGuid.html @@ -5,7 +5,7 @@ generate and set conserved guid for each spectrum data - + @@ -73,8 +73,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzDIA/taxonomy/clusters.html b/Rscript/Library/mzkit_app/vignettes/mzDIA/taxonomy/clusters.html index ddb2683fb1..7e2e7a4ad6 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzDIA/taxonomy/clusters.html +++ b/Rscript/Library/mzkit_app/vignettes/mzDIA/taxonomy/clusters.html @@ -5,7 +5,7 @@ get spectrum clusters - + @@ -63,8 +63,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzDIA/taxonomy/parallel_tree.html b/Rscript/Library/mzkit_app/vignettes/mzDIA/taxonomy/parallel_tree.html index 5dce303557..d0041d2fc9 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzDIA/taxonomy/parallel_tree.html +++ b/Rscript/Library/mzkit_app/vignettes/mzDIA/taxonomy/parallel_tree.html @@ -5,7 +5,7 @@ create taxonomy tree for multiple sample data in parallel - + @@ -89,8 +89,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzDIA/taxonomy/tree.html b/Rscript/Library/mzkit_app/vignettes/mzDIA/taxonomy/tree.html index 76a45db58d..2a236b297b 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzDIA/taxonomy/tree.html +++ b/Rscript/Library/mzkit_app/vignettes/mzDIA/taxonomy/tree.html @@ -5,7 +5,7 @@ create a spectrum taxonomy tree object - + @@ -64,8 +64,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzDIA/taxonomy/vocabulary.html b/Rscript/Library/mzkit_app/vignettes/mzDIA/taxonomy/vocabulary.html index ad3f02f40d..f89848d8ab 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzDIA/taxonomy/vocabulary.html +++ b/Rscript/Library/mzkit_app/vignettes/mzDIA/taxonomy/vocabulary.html @@ -5,7 +5,7 @@ vocabulary - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/GCMS/ROIlist.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/GCMS/ROIlist.html index 45ba4c5ae0..cf7e9809b3 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/GCMS/ROIlist.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/GCMS/ROIlist.html @@ -5,7 +5,7 @@ do peak detection for gc-ms rawdata - + @@ -84,8 +84,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/GCMS/SIMIonExtractor.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/GCMS/SIMIonExtractor.html index cc97a33384..8edcab0a8c 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/GCMS/SIMIonExtractor.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/GCMS/SIMIonExtractor.html @@ -5,7 +5,7 @@ SIMIonExtractor - + @@ -64,8 +64,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/GCMS/ScanIonExtractor.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/GCMS/ScanIonExtractor.html index 317c021154..c345ce1974 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/GCMS/ScanIonExtractor.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/GCMS/ScanIonExtractor.html @@ -5,7 +5,7 @@ ScanIonExtractor - + @@ -64,8 +64,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/GCMS/as.quantify.ion.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/GCMS/as.quantify.ion.html index 354759aff5..6562aeafbf 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/GCMS/as.quantify.ion.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/GCMS/as.quantify.ion.html @@ -5,7 +5,7 @@ as.quantify.ion - + @@ -61,8 +61,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/GCMS/contentTable.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/GCMS/contentTable.html index a15e8dc3db..a4eea732a3 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/GCMS/contentTable.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/GCMS/contentTable.html @@ -5,7 +5,7 @@ contentTable - + @@ -61,8 +61,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/GCMS/linear_algorithm.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/GCMS/linear_algorithm.html index 8ad617558a..8cd0a0cc2d 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/GCMS/linear_algorithm.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/GCMS/linear_algorithm.html @@ -5,7 +5,7 @@ create linear model handler - + @@ -70,8 +70,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/GCMS/linears.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/GCMS/linears.html index 35d2f079ad..4585071b30 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/GCMS/linears.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/GCMS/linears.html @@ -5,7 +5,7 @@ linears - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/GCMS/parseContents.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/GCMS/parseContents.html index fa66775977..3514ebec66 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/GCMS/parseContents.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/GCMS/parseContents.html @@ -5,7 +5,7 @@ parseContents - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/GCMS/peakRaw.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/GCMS/peakRaw.html index b4f7da03dc..f970379775 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/GCMS/peakRaw.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/GCMS/peakRaw.html @@ -5,7 +5,7 @@ read raw peaks data - + @@ -68,8 +68,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/GCMS/read.raw.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/GCMS/read.raw.html index 9f09466f97..22f87a0827 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/GCMS/read.raw.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/GCMS/read.raw.html @@ -5,7 +5,7 @@ read gcms rawdata - + @@ -63,8 +63,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/Linears/ionPeaks.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/Linears/ionPeaks.html index f012a439d7..6efb971049 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/Linears/ionPeaks.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/Linears/ionPeaks.html @@ -5,7 +5,7 @@ get ions peaks - + @@ -67,8 +67,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/Linears/lines.table.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/Linears/lines.table.html index 868429305a..a68e3d7671 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/Linears/lines.table.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/Linears/lines.table.html @@ -5,7 +5,7 @@ export the table data of the reference linears - + @@ -63,8 +63,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/Linears/points.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/Linears/points.html index 9967a71884..a458177c4f 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/Linears/points.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/Linears/points.html @@ -5,7 +5,7 @@ Get reference input points - + @@ -67,8 +67,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/Linears/quantify.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/Linears/quantify.html index 312de15702..1238f3cee3 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/Linears/quantify.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/Linears/quantify.html @@ -5,7 +5,7 @@ Run sample data quantify - + @@ -71,8 +71,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/Linears/read.linearPack.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/Linears/read.linearPack.html index 8779ebbb69..23c0037e2a 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/Linears/read.linearPack.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/Linears/read.linearPack.html @@ -5,7 +5,7 @@ read.linearPack - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/Linears/report.dataset.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/Linears/report.dataset.html index 73b4ace42f..810fbead2d 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/Linears/report.dataset.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/Linears/report.dataset.html @@ -5,7 +5,7 @@ Create targeted linear dataset object for do linear quantification data report. - + @@ -89,8 +89,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/Linears/result.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/Linears/result.html index a636d38b05..6fb08ee3af 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/Linears/result.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/Linears/result.html @@ -5,7 +5,7 @@ Get quantify result - + @@ -63,8 +63,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/Linears/scans.X.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/Linears/scans.X.html index 0f395b72c4..85c1651a2a 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/Linears/scans.X.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/Linears/scans.X.html @@ -5,7 +5,7 @@ Get result of ``AIS/At`` - + @@ -63,8 +63,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/Linears/write.ionPeaks.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/Linears/write.ionPeaks.html index 30630dff95..7f11de4b4b 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/Linears/write.ionPeaks.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/Linears/write.ionPeaks.html @@ -5,7 +5,7 @@ Write peak data which is extract from the raw file with - + @@ -67,8 +67,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/Linears/write.points.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/Linears/write.points.html index 17ddd7873b..a775650714 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/Linears/write.points.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/Linears/write.points.html @@ -5,7 +5,7 @@ save reference point data into a given table file - + @@ -67,8 +67,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/MRM.arguments.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/MRM.arguments.html index 300db290ef..5d038d00ad 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/MRM.arguments.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/MRM.arguments.html @@ -5,7 +5,7 @@ Create argument object for run MRM quantification. - + @@ -108,8 +108,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/MRM.peak2.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/MRM.peak2.html index fc53560320..abab08b653 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/MRM.peak2.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/MRM.peak2.html @@ -5,7 +5,7 @@ Get MRM ions peaks data from a given raw data file - + @@ -72,8 +72,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/MRM.peaks.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/MRM.peaks.html index 791cb6f646..97fbc8eae5 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/MRM.peaks.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/MRM.peaks.html @@ -5,7 +5,7 @@ Get MRM ions peaks data from a given raw data file - + @@ -116,8 +116,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/MRM.rt_alignments.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/MRM.rt_alignments.html index bc2e463bc6..f361d30d0d 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/MRM.rt_alignments.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/MRM.rt_alignments.html @@ -5,7 +5,7 @@ MRM.rt_alignments - + @@ -61,8 +61,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/R2.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/R2.html index 3dc729ad40..d923637c2f 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/R2.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/R2.html @@ -5,7 +5,7 @@ R2 - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/as.ion_pairs.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/as.ion_pairs.html index 2fee088228..2b236fc1d7 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/as.ion_pairs.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/as.ion_pairs.html @@ -5,7 +5,7 @@ Convert any compatibale type as the ion pairs data object for MRM target selected. - + @@ -67,8 +67,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/extract.ions.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/extract.ions.html index 92d3cb350b..e8ad91e07d 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/extract.ions.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/extract.ions.html @@ -5,7 +5,7 @@ Extract ion peaks - + @@ -68,8 +68,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/extract.peakROI.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/extract.peakROI.html index 4a078b2484..505ce15205 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/extract.peakROI.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/extract.peakROI.html @@ -5,7 +5,7 @@ Exact ``regions of interested`` based on the given ion pair as targets. - + @@ -95,8 +95,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/extract_ionpairs.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/extract_ionpairs.html index b5215b8d0f..6d7b0b4032 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/extract_ionpairs.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/extract_ionpairs.html @@ -5,7 +5,7 @@ Extract all ion pairs information from the given rawdata file - + @@ -67,8 +67,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/extract_mrm.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/extract_mrm.html index 25106bfe82..a9fd36fb1a 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/extract_mrm.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/extract_mrm.html @@ -5,7 +5,7 @@ Extract ion peaks - + @@ -68,8 +68,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/find_untargeted_ionpair.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/find_untargeted_ionpair.html index 3a15f5ecaa..1f06041c90 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/find_untargeted_ionpair.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/find_untargeted_ionpair.html @@ -5,7 +5,7 @@ MRM-Ion Pair Finder is used to automatically and systematically define MRM transitions from untargeted metabolomics data. - + @@ -70,8 +70,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/isomerism.ion_pairs.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/isomerism.ion_pairs.html index ec3c4b9b6a..8df1cbbcc5 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/isomerism.ion_pairs.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/isomerism.ion_pairs.html @@ -5,7 +5,7 @@ isomerism.ion_pairs - + @@ -61,8 +61,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/linears.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/linears.html index 6587c24c6c..6356824237 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/linears.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/linears.html @@ -5,7 +5,7 @@ Create linear fitting based on the wiff raw scan data. - + @@ -84,8 +84,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/read.IS.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/read.IS.html index 5c8064a044..aa66cfffd3 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/read.IS.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/read.IS.html @@ -5,7 +5,7 @@ Read the definition of internal standards - + @@ -68,8 +68,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/read.ion_pairs.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/read.ion_pairs.html index d5a26d9d46..78ae2984e2 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/read.ion_pairs.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/read.ion_pairs.html @@ -5,7 +5,7 @@ Get ion pair definition data from a given table file. - + @@ -68,8 +68,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/read.reference.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/read.reference.html index 417046ee3f..e456412f64 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/read.reference.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/read.reference.html @@ -5,7 +5,7 @@ Read reference points - + @@ -68,8 +68,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/sample.quantify.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/sample.quantify.html index d789ac2ded..e74ade5e33 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/sample.quantify.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/sample.quantify.html @@ -5,7 +5,7 @@ Do sample quantify - + @@ -79,8 +79,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/sample.quantify2.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/sample.quantify2.html index 69432f6aab..fe59721cc7 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/sample.quantify2.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/sample.quantify2.html @@ -5,7 +5,7 @@ Do sample quantify - + @@ -71,8 +71,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/wiff.rawfiles.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/wiff.rawfiles.html index 0a1313a888..18965e5b39 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/wiff.rawfiles.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/wiff.rawfiles.html @@ -5,7 +5,7 @@ Create model of the MRM raw files - + @@ -79,8 +79,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/wiff.scan2.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/wiff.scan2.html index da7c525605..f477232d59 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/wiff.scan2.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/wiff.scan2.html @@ -5,7 +5,7 @@ Scan the raw file data - + @@ -88,8 +88,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/wiff.scans.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/wiff.scans.html index 6a44a4f320..b20c61470f 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/wiff.scans.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/MRMLinear/wiff.scans.html @@ -5,7 +5,7 @@ Scan the raw file data - + @@ -98,8 +98,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/math/chromatogram.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/math/chromatogram.html index 71b5270efe..8c49cec5ca 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/math/chromatogram.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/math/chromatogram.html @@ -5,7 +5,7 @@ Create a chromatogram data from a dataframe object - + @@ -79,8 +79,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/math/peakROI.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/math/peakROI.html index 22d4284fe0..0e570c3690 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/math/peakROI.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/math/peakROI.html @@ -5,7 +5,7 @@ Peak finding - + @@ -88,8 +88,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/math/preprocessing.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/math/preprocessing.html index c2e9d1a93f..8007bf755a 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/math/preprocessing.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/math/preprocessing.html @@ -5,7 +5,7 @@ data matrix pre-processing before run data analysis - + @@ -64,8 +64,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/math/removes_missing.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/math/removes_missing.html index 706232b205..b559896505 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/math/removes_missing.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/math/removes_missing.html @@ -5,7 +5,7 @@ removes the missing peaks - + @@ -75,8 +75,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/math/resample.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/math/resample.html index 1f4bf0babc..ddb3c5ab4d 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/math/resample.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/math/resample.html @@ -5,7 +5,7 @@ Do resample of the chromatogram data - + @@ -69,8 +69,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/MS1deconv.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/MS1deconv.html index 34790d509c..e19f68dda2 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/MS1deconv.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/MS1deconv.html @@ -5,7 +5,7 @@ A debug function for test peak finding method - + @@ -73,8 +73,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/RI_batch_join.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/RI_batch_join.html index 0e33ab5449..bacdf0592b 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/RI_batch_join.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/RI_batch_join.html @@ -5,7 +5,7 @@ make peaktable join of two batch data via (mz,RI) - + @@ -70,8 +70,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/RI_cal.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/RI_cal.html index 3e878f2d45..eaf833ef3f 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/RI_cal.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/RI_cal.html @@ -5,7 +5,7 @@ RI calculation of a speicifc sample data - + @@ -81,8 +81,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/RI_reference.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/RI_reference.html index 11e759081b..affbd3abb9 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/RI_reference.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/RI_reference.html @@ -5,7 +5,7 @@ Create RI reference dataset. - + @@ -62,8 +62,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/adjust_to_seconds.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/adjust_to_seconds.html index 65e6770484..e029f9709e 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/adjust_to_seconds.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/adjust_to_seconds.html @@ -5,7 +5,7 @@ adjust the reteintion time data to unit seconds - + @@ -67,8 +67,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/as.peak_set.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/as.peak_set.html index aaeb7a8861..13397ed19e 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/as.peak_set.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/as.peak_set.html @@ -5,7 +5,7 @@ cast dataset to mzkit peaktable object - + @@ -77,8 +77,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/find_xcms_ionPeaks.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/find_xcms_ionPeaks.html index 0a2df0e607..1ebd6f18f3 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/find_xcms_ionPeaks.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/find_xcms_ionPeaks.html @@ -5,7 +5,7 @@ helper function for find ms1 peaks based on the given mz/rt tuple data - + @@ -83,8 +83,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/get_xcms_ionPeaks.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/get_xcms_ionPeaks.html index b6618d36cf..3241628e6f 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/get_xcms_ionPeaks.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/get_xcms_ionPeaks.html @@ -5,7 +5,7 @@ get ion peaks via the unique reference id - + @@ -78,8 +78,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/mz.groups.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/mz.groups.html index 92cd959d65..79873ae5fc 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/mz.groups.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/mz.groups.html @@ -5,7 +5,7 @@ do ``m/z`` grouping under the given tolerance - + @@ -83,8 +83,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/mz_deco.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/mz_deco.html index 88092ca3a2..aa4911a0fa 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/mz_deco.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/mz_deco.html @@ -5,7 +5,7 @@ Chromatogram data deconvolution - + @@ -99,8 +99,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/peak_alignment.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/peak_alignment.html index 711242f6c6..db1c704fd4 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/peak_alignment.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/peak_alignment.html @@ -5,7 +5,7 @@ Do COW peak alignment and export peaktable - + @@ -87,8 +87,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/peak_subset.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/peak_subset.html index 61f0db565f..9c717bde33 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/peak_subset.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/peak_subset.html @@ -5,7 +5,7 @@ make sample column projection - + @@ -69,8 +69,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/pull_xic.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/pull_xic.html index 5ac51c9a3b..a9e5fbf17e 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/pull_xic.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/pull_xic.html @@ -5,7 +5,7 @@ extract a collection of xic data for a specific ion feature - + @@ -96,8 +96,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/read.peakFeatures.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/read.peakFeatures.html index 73fc178b45..ef782535d0 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/read.peakFeatures.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/read.peakFeatures.html @@ -5,7 +5,7 @@ read the peak feature table data - + @@ -69,8 +69,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/read.rt_shifts.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/read.rt_shifts.html index 8d8dcc8800..e14f2e76a3 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/read.rt_shifts.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/read.rt_shifts.html @@ -5,7 +5,7 @@ read.rt_shifts - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/read.xcms_features.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/read.xcms_features.html index 43fea9c355..4f6f0e855d 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/read.xcms_features.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/read.xcms_features.html @@ -5,7 +5,7 @@ Try to cast the dataframe to the mzkit peak feature object set - + @@ -63,8 +63,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/read.xcms_peaks.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/read.xcms_peaks.html index 4f55af704e..38abbdacbe 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/read.xcms_peaks.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/read.xcms_peaks.html @@ -5,7 +5,7 @@ read the peaktable file that in xcms2 output format - + @@ -70,8 +70,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/to_expression.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/to_expression.html index 8ac70f9137..32448248e9 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/to_expression.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/to_expression.html @@ -5,7 +5,7 @@ cast peaktable to expression matrix object - + @@ -63,8 +63,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/to_matrix.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/to_matrix.html index c003a5af28..e5b1340cde 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/to_matrix.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/to_matrix.html @@ -5,7 +5,7 @@ cast peaktable to mzkit expression matrix - + @@ -63,8 +63,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/write.peaks.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/write.peaks.html index 9d0029d894..fe3b565367 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/write.peaks.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/write.peaks.html @@ -5,7 +5,7 @@ write peak debug data - + @@ -71,8 +71,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/write.xcms_peaks.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/write.xcms_peaks.html index 2d1ab546b2..ed3c732cf7 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/write.xcms_peaks.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/write.xcms_peaks.html @@ -5,7 +5,7 @@ save mzkit peaktable object to csv table file - + @@ -67,8 +67,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/xcms_peak.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/xcms_peak.html index fa11c03935..5bde30dfac 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/xcms_peak.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/xcms_peak.html @@ -5,7 +5,7 @@ Create a xcms peak data object - + @@ -91,8 +91,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/xic_pool.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/xic_pool.html index fffdf0170d..e6b8b11ee2 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/xic_pool.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/mzDeco/xic_pool.html @@ -5,7 +5,7 @@ Load xic sample data files - + @@ -63,8 +63,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/visualPlots/MRM.chromatogramPeaks.plot.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/visualPlots/MRM.chromatogramPeaks.plot.html index ba7292521c..280af71970 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/visualPlots/MRM.chromatogramPeaks.plot.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/visualPlots/MRM.chromatogramPeaks.plot.html @@ -5,7 +5,7 @@ Visualization plot of the MRM chromatogram peaks data. - + @@ -101,8 +101,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/visualPlots/chromatogram.plot.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/visualPlots/chromatogram.plot.html index 53042571c1..5c3b802330 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/visualPlots/chromatogram.plot.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/visualPlots/chromatogram.plot.html @@ -5,7 +5,7 @@ plot MRM chromatogram overlaps in a speicifc rawdata file - + @@ -72,8 +72,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/visualPlots/standard_curve.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/visualPlots/standard_curve.html index a58e0b3a7c..acb3572e75 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/visualPlots/standard_curve.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/visualPlots/standard_curve.html @@ -5,7 +5,7 @@ Draw standard curve - + @@ -80,8 +80,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mz_quantify/xcms/parse_xcms_samples.html b/Rscript/Library/mzkit_app/vignettes/mz_quantify/xcms/parse_xcms_samples.html index dd119c0d30..c607326b40 100644 --- a/Rscript/Library/mzkit_app/vignettes/mz_quantify/xcms/parse_xcms_samples.html +++ b/Rscript/Library/mzkit_app/vignettes/mz_quantify/xcms/parse_xcms_samples.html @@ -5,7 +5,7 @@ parse_xcms_samples - + @@ -61,8 +61,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/GCxGC/TIC1D.html b/Rscript/Library/mzkit_app/vignettes/mzkit/GCxGC/TIC1D.html index b87341eb78..76b51a407e 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/GCxGC/TIC1D.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/GCxGC/TIC1D.html @@ -5,7 +5,7 @@ TIC1D - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/GCxGC/TIC2D.html b/Rscript/Library/mzkit_app/vignettes/mzkit/GCxGC/TIC2D.html index 432aea64af..b3257115a0 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/GCxGC/TIC2D.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/GCxGC/TIC2D.html @@ -5,7 +5,7 @@ Demodulate the 1D TIC to 2D data - + @@ -69,8 +69,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/GCxGC/demodulate_2D.html b/Rscript/Library/mzkit_app/vignettes/mzkit/GCxGC/demodulate_2D.html index e28db8aad3..d2c59f918f 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/GCxGC/demodulate_2D.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/GCxGC/demodulate_2D.html @@ -5,7 +5,7 @@ Demodulate the 1D rawdata input as 2D data - + @@ -78,8 +78,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/GCxGC/extract_2D_peaks.html b/Rscript/Library/mzkit_app/vignettes/mzkit/GCxGC/extract_2D_peaks.html index da334db29a..82e579bf54 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/GCxGC/extract_2D_peaks.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/GCxGC/extract_2D_peaks.html @@ -5,7 +5,7 @@ make 2d peak detection and extract the related peak feature ROI set - + @@ -65,8 +65,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/GCxGC/extract_xic_layer.html b/Rscript/Library/mzkit_app/vignettes/mzkit/GCxGC/extract_xic_layer.html index 3746b19b05..2f351ccf30 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/GCxGC/extract_xic_layer.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/GCxGC/extract_xic_layer.html @@ -5,7 +5,7 @@ extract GCxGC 2d peaks from the mzpack raw data file - + @@ -76,8 +76,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/GCxGC/read.cdf.html b/Rscript/Library/mzkit_app/vignettes/mzkit/GCxGC/read.cdf.html index bc00176bc7..abc97c78aa 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/GCxGC/read.cdf.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/GCxGC/read.cdf.html @@ -5,7 +5,7 @@ read GCxGC 2D Chromatogram data from a given netcdf file. - + @@ -67,8 +67,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/GCxGC/save.cdf.html b/Rscript/Library/mzkit_app/vignettes/mzkit/GCxGC/save.cdf.html index 19ab1ea831..887b5581b1 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/GCxGC/save.cdf.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/GCxGC/save.cdf.html @@ -5,7 +5,7 @@ save GCxGC 2D Chromatogram data as a new netcdf file. - + @@ -71,8 +71,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/InChI/get_formula.html b/Rscript/Library/mzkit_app/vignettes/mzkit/InChI/get_formula.html index 86f1422c0f..10c827ddec 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/InChI/get_formula.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/InChI/get_formula.html @@ -5,7 +5,7 @@ get_formula - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/InChI/get_struct.html b/Rscript/Library/mzkit_app/vignettes/mzkit/InChI/get_struct.html index 97d85a7c71..0934ffa06c 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/InChI/get_struct.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/InChI/get_struct.html @@ -5,7 +5,7 @@ get_struct - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/InChI/inchikey.html b/Rscript/Library/mzkit_app/vignettes/mzkit/InChI/inchikey.html index c368d4f43d..9cd0226689 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/InChI/inchikey.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/InChI/inchikey.html @@ -5,7 +5,7 @@ inchikey - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/InChI/parse.html b/Rscript/Library/mzkit_app/vignettes/mzkit/InChI/parse.html index 49a9c16bde..cf2273eee2 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/InChI/parse.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/InChI/parse.html @@ -5,7 +5,7 @@ parse the inchi string - + @@ -97,8 +97,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/MSI_summary.html b/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/MSI_summary.html index 78de36cdf0..ba3140eca4 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/MSI_summary.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/MSI_summary.html @@ -5,7 +5,7 @@ Fetch MSI summary data - + @@ -87,8 +87,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/as.layer.html b/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/as.layer.html index ac50fe6f29..c033869e46 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/as.layer.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/as.layer.html @@ -5,7 +5,7 @@ cast the pixel collection to a ion imaging layer data - + @@ -98,8 +98,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/basePeakMz.html b/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/basePeakMz.html index 783b6299b7..8a170bfa9e 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/basePeakMz.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/basePeakMz.html @@ -5,7 +5,7 @@ Get the mass spectrum data of the MSI base peak data - + @@ -63,8 +63,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/cast.spatial_layers.html b/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/cast.spatial_layers.html index 9c8f06b25b..8ccb873728 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/cast.spatial_layers.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/cast.spatial_layers.html @@ -5,7 +5,7 @@ cast the rawdata matrix as the ms-imaging ion layer - + @@ -73,8 +73,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/correction.html b/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/correction.html index 3bc61e87a1..296b05eff1 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/correction.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/correction.html @@ -5,7 +5,7 @@ calculate the X axis scale - + @@ -80,8 +80,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/dimension_size.html b/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/dimension_size.html index b8046b2c5e..228b9b1d9c 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/dimension_size.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/dimension_size.html @@ -5,7 +5,7 @@ get or set the dimension size of the ms-imaging mzpack raw data object - + @@ -80,8 +80,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/getMatrixIons.html b/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/getMatrixIons.html index 9f95ab28eb..27afe1cf76 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/getMatrixIons.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/getMatrixIons.html @@ -5,7 +5,7 @@ get matrix ions feature m/z vector - + @@ -88,8 +88,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/ionStat.html b/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/ionStat.html index 0a0063b9b3..10a54b9cae 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/ionStat.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/ionStat.html @@ -5,7 +5,7 @@ Extract the ion features inside a MSI raw data slide sample file - + @@ -79,8 +79,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/ions_jointmatrix.html b/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/ions_jointmatrix.html index 796048d935..b740b80b49 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/ions_jointmatrix.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/ions_jointmatrix.html @@ -5,7 +5,7 @@ ions_jointmatrix - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/levels.convolution.html b/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/levels.convolution.html index 435e5ead76..2983d7e447 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/levels.convolution.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/levels.convolution.html @@ -5,7 +5,7 @@ sum pixels for create pixel spot convolution - + @@ -67,8 +67,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/moran_I.html b/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/moran_I.html index 7c1948639e..9ac35dc5d5 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/moran_I.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/moran_I.html @@ -5,7 +5,7 @@ evaluate the moran index for each ion layer - + @@ -66,8 +66,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/msi_metadata.html b/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/msi_metadata.html index fbd88da1bd..8b791e1aba 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/msi_metadata.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/msi_metadata.html @@ -5,7 +5,7 @@ get ms-imaging metadata - + @@ -68,8 +68,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/open.imzML.html b/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/open.imzML.html index fba6dd6e74..561f0fd468 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/open.imzML.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/open.imzML.html @@ -5,7 +5,7 @@ open the reader for the imzML ms-imaging file - + @@ -73,8 +73,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/pack_matrix.html b/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/pack_matrix.html index 554ed5ea4b..3d055a7409 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/pack_matrix.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/pack_matrix.html @@ -5,7 +5,7 @@ pack the matrix file as the MSI mzpack - + @@ -73,8 +73,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/peakMatrix.html b/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/peakMatrix.html index 9beaf559d2..9306255c1f 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/peakMatrix.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/peakMatrix.html @@ -5,7 +5,7 @@ Extract the ion data matrix - + @@ -94,8 +94,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/peakSamples.html b/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/peakSamples.html index 6cc9995984..b4974838fa 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/peakSamples.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/peakSamples.html @@ -5,7 +5,7 @@ split the raw MSI 2D data into multiple parts with given resolution parts - + @@ -82,8 +82,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/pixelId.html b/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/pixelId.html index da241a1c1a..ac9a5c0984 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/pixelId.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/pixelId.html @@ -5,7 +5,7 @@ get pixels [x,y] tags collection for a specific ion - + @@ -79,8 +79,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/pixelIons.html b/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/pixelIons.html index 2cf1e7eaa7..1c025d25ac 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/pixelIons.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/pixelIons.html @@ -5,7 +5,7 @@ get number of ions in each pixel scans - + @@ -63,8 +63,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/pixelMatrix.html b/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/pixelMatrix.html index 86ab9f3ca1..82d8c12376 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/pixelMatrix.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/pixelMatrix.html @@ -5,7 +5,7 @@ dumping raw data matrix as text table file. - + @@ -89,8 +89,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/pixels.html b/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/pixels.html index 23322fb8c0..fc01a9466d 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/pixels.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/pixels.html @@ -5,7 +5,7 @@ get pixels size from the raw data file - + @@ -79,8 +79,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/raster.html b/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/raster.html index e0b69b7d0e..53d7732051 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/raster.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/raster.html @@ -5,7 +5,7 @@ cast the ms-imaging layer data to raster object - + @@ -73,8 +73,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/row.scans.html b/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/row.scans.html index 6bd2c9b294..aa28091bec 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/row.scans.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/row.scans.html @@ -5,7 +5,7 @@ each raw data file is a row scan data - + @@ -79,8 +79,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/sample_bootstraping.html b/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/sample_bootstraping.html index 7553d1ef80..f0eca6c2a7 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/sample_bootstraping.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/sample_bootstraping.html @@ -5,7 +5,7 @@ make expression bootstrapping of current ion layer - + @@ -87,8 +87,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/scale.html b/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/scale.html index 50b74e3701..2fb1e08d96 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/scale.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/scale.html @@ -5,7 +5,7 @@ scale the spatial matrix by column - + @@ -85,8 +85,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/scanMatrix.html b/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/scanMatrix.html index c33274843b..a45b514566 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/scanMatrix.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/scanMatrix.html @@ -5,7 +5,7 @@ combine each row scan summary vector as the pixels 2D matrix - + @@ -67,8 +67,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/scans2D.html b/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/scans2D.html index c702688599..b736592cda 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/scans2D.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/scans2D.html @@ -5,7 +5,7 @@ combine each row scan raw data files as the pixels 2D matrix - + @@ -74,8 +74,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/spatial.convolution.html b/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/spatial.convolution.html index 7addf9e8d9..c255d165ef 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/spatial.convolution.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/spatial.convolution.html @@ -5,7 +5,7 @@ sum pixels for create pixel spot convolution - + @@ -67,8 +67,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/splice.html b/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/splice.html index e374df7f8c..18fd6970ba 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/splice.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/splice.html @@ -5,7 +5,7 @@ split the raw 2D MSI data into multiple parts with given parts - + @@ -72,8 +72,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/write.imzML.html b/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/write.imzML.html index e0b18d5691..90d3116754 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/write.imzML.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/MSI/write.imzML.html @@ -5,7 +5,7 @@ Save and write the given ms-imaging mzpack object as imzML file - + @@ -86,8 +86,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/Mummichog/candidates_Id.html b/Rscript/Library/mzkit_app/vignettes/mzkit/Mummichog/candidates_Id.html index 80c6572fd8..bed6e31a69 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/Mummichog/candidates_Id.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/Mummichog/candidates_Id.html @@ -5,7 +5,7 @@ Extract all candidates unique id from the given query result - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/Mummichog/createMzset.html b/Rscript/Library/mzkit_app/vignettes/mzkit/Mummichog/createMzset.html index 3f6d9cf87b..ea3dbd3902 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/Mummichog/createMzset.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/Mummichog/createMzset.html @@ -5,7 +5,7 @@ createMzset - + @@ -61,8 +61,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/Mummichog/fromGseaBackground.html b/Rscript/Library/mzkit_app/vignettes/mzkit/Mummichog/fromGseaBackground.html index 348219e9d4..b1e074ac79 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/Mummichog/fromGseaBackground.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/Mummichog/fromGseaBackground.html @@ -5,7 +5,7 @@ cast background models for ``peakList_annotation`` analysis based on - + @@ -68,8 +68,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/Mummichog/group_peaks.html b/Rscript/Library/mzkit_app/vignettes/mzkit/Mummichog/group_peaks.html index ee585d578f..153793d0ab 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/Mummichog/group_peaks.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/Mummichog/group_peaks.html @@ -5,7 +5,7 @@ group_peaks - + @@ -64,8 +64,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/Mummichog/kegg_background.html b/Rscript/Library/mzkit_app/vignettes/mzkit/Mummichog/kegg_background.html index bcbc9629d0..e79ad680dc 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/Mummichog/kegg_background.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/Mummichog/kegg_background.html @@ -5,7 +5,7 @@ create kegg pathway network graph background model - + @@ -68,8 +68,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/Mummichog/mzScore.html b/Rscript/Library/mzkit_app/vignettes/mzkit/Mummichog/mzScore.html index 34e658c9d1..9e4e2e369d 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/Mummichog/mzScore.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/Mummichog/mzScore.html @@ -5,7 +5,7 @@ export of the annotation score result table - + @@ -66,8 +66,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/Mummichog/peakList_annotation.html b/Rscript/Library/mzkit_app/vignettes/mzkit/Mummichog/peakList_annotation.html index 8645fe08d4..3df2942186 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/Mummichog/peakList_annotation.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/Mummichog/peakList_annotation.html @@ -5,7 +5,7 @@ do ms1 peaks annotation - + @@ -91,8 +91,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/Mummichog/queryCandidateSet.html b/Rscript/Library/mzkit_app/vignettes/mzkit/Mummichog/queryCandidateSet.html index 8934e7f024..81c451a129 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/Mummichog/queryCandidateSet.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/Mummichog/queryCandidateSet.html @@ -5,7 +5,7 @@ Matches all of the annotation hits candidates from a given of the mass peak list - + @@ -73,8 +73,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/NMR/FID.html b/Rscript/Library/mzkit_app/vignettes/mzkit/NMR/FID.html index c3425a9b13..22f0d4c891 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/NMR/FID.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/NMR/FID.html @@ -5,7 +5,7 @@ Read Free Induction Decay data matrix - + @@ -63,8 +63,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/NMR/acquisition.html b/Rscript/Library/mzkit_app/vignettes/mzkit/NMR/acquisition.html index 4fa27015a6..0f6bc04067 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/NMR/acquisition.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/NMR/acquisition.html @@ -5,7 +5,7 @@ get all acquisition data in the raw data file - + @@ -63,8 +63,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/NMR/nmr_dft.html b/Rscript/Library/mzkit_app/vignettes/mzkit/NMR/nmr_dft.html index e0c321d99d..f75b5aa1ca 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/NMR/nmr_dft.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/NMR/nmr_dft.html @@ -5,7 +5,7 @@ nmr_dft - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/NMR/read.nmrML.html b/Rscript/Library/mzkit_app/vignettes/mzkit/NMR/read.nmrML.html index 88873e4f86..9aaff0ed57 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/NMR/read.nmrML.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/NMR/read.nmrML.html @@ -5,7 +5,7 @@ read.nmrML - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/NMR/spectrum.html b/Rscript/Library/mzkit_app/vignettes/mzkit/NMR/spectrum.html index d013e5e590..aa398da6a2 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/NMR/spectrum.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/NMR/spectrum.html @@ -5,7 +5,7 @@ - + @@ -67,8 +67,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/NMR/spectrumList.html b/Rscript/Library/mzkit_app/vignettes/mzkit/NMR/spectrumList.html index 8ac9e87f73..e80e6453d6 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/NMR/spectrumList.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/NMR/spectrumList.html @@ -5,7 +5,7 @@ spectrumList - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/ProteoWizard/MRM.mzML.html b/Rscript/Library/mzkit_app/vignettes/mzkit/ProteoWizard/MRM.mzML.html index ca22bfd9f5..a7463d91fc 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/ProteoWizard/MRM.mzML.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/ProteoWizard/MRM.mzML.html @@ -5,7 +5,7 @@ Convert MRM wiff file to mzMl files - + @@ -64,8 +64,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/ProteoWizard/convert.thermo.raw.html b/Rscript/Library/mzkit_app/vignettes/mzkit/ProteoWizard/convert.thermo.raw.html index ec8696226e..49770c59e4 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/ProteoWizard/convert.thermo.raw.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/ProteoWizard/convert.thermo.raw.html @@ -5,7 +5,7 @@ Convert thermo raw files to mzXML files - + @@ -78,8 +78,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/ProteoWizard/filter.msLevel.html b/Rscript/Library/mzkit_app/vignettes/mzkit/ProteoWizard/filter.msLevel.html index 479e3991c9..91df14d511 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/ProteoWizard/filter.msLevel.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/ProteoWizard/filter.msLevel.html @@ -5,7 +5,7 @@ filter.msLevel - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/ProteoWizard/filter.scanTime.html b/Rscript/Library/mzkit_app/vignettes/mzkit/ProteoWizard/filter.scanTime.html index b8acb43288..ff27158215 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/ProteoWizard/filter.scanTime.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/ProteoWizard/filter.scanTime.html @@ -5,7 +5,7 @@ - + @@ -67,8 +67,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/ProteoWizard/msconvert.ready.html b/Rscript/Library/mzkit_app/vignettes/mzkit/ProteoWizard/msconvert.ready.html index 048d527c89..b7f2acfafe 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/ProteoWizard/msconvert.ready.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/ProteoWizard/msconvert.ready.html @@ -5,7 +5,7 @@ Is the ``ProteoWizard`` program ready to use? - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/RamanSpectroscopy/readFile.html b/Rscript/Library/mzkit_app/vignettes/mzkit/RamanSpectroscopy/readFile.html index a62c94990a..3b1191583a 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/RamanSpectroscopy/readFile.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/RamanSpectroscopy/readFile.html @@ -5,7 +5,7 @@ parse the Raman Spectroscopy data from a text file - + @@ -67,8 +67,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/SMILES/as.formula.html b/Rscript/Library/mzkit_app/vignettes/mzkit/SMILES/as.formula.html index 16c2646358..a41aa06081 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/SMILES/as.formula.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/SMILES/as.formula.html @@ -5,7 +5,7 @@ as.formula - + @@ -61,8 +61,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/SMILES/as.graph.html b/Rscript/Library/mzkit_app/vignettes/mzkit/SMILES/as.graph.html index 46f21cd86f..120244c0d8 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/SMILES/as.graph.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/SMILES/as.graph.html @@ -5,7 +5,7 @@ as.graph - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/SMILES/atoms.html b/Rscript/Library/mzkit_app/vignettes/mzkit/SMILES/atoms.html index 481af330ca..2e2b24be82 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/SMILES/atoms.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/SMILES/atoms.html @@ -5,7 +5,7 @@ get atoms table from the SMILES structure data - + @@ -63,8 +63,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/SMILES/links.html b/Rscript/Library/mzkit_app/vignettes/mzkit/SMILES/links.html index a59654394f..f55050fca7 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/SMILES/links.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/SMILES/links.html @@ -5,7 +5,7 @@ create graph embedding result for a specific molecular strucutre data - + @@ -82,8 +82,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/SMILES/parse.html b/Rscript/Library/mzkit_app/vignettes/mzkit/SMILES/parse.html index 3cfb50869d..e95cc9224d 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/SMILES/parse.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/SMILES/parse.html @@ -5,7 +5,7 @@ Parse the SMILES molecule structre string - + @@ -72,8 +72,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/SMILES/score.html b/Rscript/Library/mzkit_app/vignettes/mzkit/SMILES/score.html index efa7e0d916..484167adcb 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/SMILES/score.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/SMILES/score.html @@ -5,7 +5,7 @@ evaluate the similarity score between two molecular strcuture - + @@ -82,8 +82,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/SCM_ionStat.html b/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/SCM_ionStat.html index 983466898f..0991e9901a 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/SCM_ionStat.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/SCM_ionStat.html @@ -5,7 +5,7 @@ do statistics of the single cell metabolomics ions features - + @@ -73,8 +73,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/TrIQ_clip.html b/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/TrIQ_clip.html index 5a470ac7ed..627ba1cf8b 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/TrIQ_clip.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/TrIQ_clip.html @@ -5,7 +5,7 @@ processing of the intensity value clip via TrIQ algorithm for the feature matrix - + @@ -73,8 +73,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/apply.scale.html b/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/apply.scale.html index 7e5f49c7ab..f5c04f6b7f 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/apply.scale.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/apply.scale.html @@ -5,7 +5,7 @@ scale matrix for each spot/cell sample - + @@ -77,8 +77,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/as.expression.html b/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/as.expression.html index e62ca6773a..50b00ae605 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/as.expression.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/as.expression.html @@ -5,7 +5,7 @@ Cast the ion feature matrix as the GCModeller expression matrix object - + @@ -69,8 +69,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/cell_clusters.html b/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/cell_clusters.html index 69ff081361..41699f7265 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/cell_clusters.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/cell_clusters.html @@ -5,7 +5,7 @@ export the cell clustering result - + @@ -64,8 +64,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/cell_embedding.html b/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/cell_embedding.html index cc6c882b09..5022facec8 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/cell_embedding.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/cell_embedding.html @@ -5,7 +5,7 @@ create a session for create spot cell embedding - + @@ -79,8 +79,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/cell_matrix.html b/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/cell_matrix.html index 5302ae56dd..de1d8c27b7 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/cell_matrix.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/cell_matrix.html @@ -5,7 +5,7 @@ export single cell expression matrix from the raw data scans - + @@ -79,8 +79,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/df.mz_matrix.html b/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/df.mz_matrix.html index 3a45500f57..d0f43778c3 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/df.mz_matrix.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/df.mz_matrix.html @@ -5,7 +5,7 @@ cast matrix object to the R liked dataframe object - + @@ -76,8 +76,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/embedding_sample.html b/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/embedding_sample.html index 91a55976dd..64b4fbb38e 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/embedding_sample.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/embedding_sample.html @@ -5,7 +5,7 @@ push a sample data into the embedding session - + @@ -77,8 +77,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/mz_matrix.html b/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/mz_matrix.html index 34eee4dfe8..289937e8e3 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/mz_matrix.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/mz_matrix.html @@ -5,7 +5,7 @@ cast the matrix object as the dataframe - + @@ -71,8 +71,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/open.matrix.html b/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/open.matrix.html index c43769dffd..24cd31ba46 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/open.matrix.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/open.matrix.html @@ -5,7 +5,7 @@ open a single cell data matrix reader - + @@ -76,8 +76,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/read.mz_matrix.html b/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/read.mz_matrix.html index 7c6262fed7..e58da1d4db 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/read.mz_matrix.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/read.mz_matrix.html @@ -5,7 +5,7 @@ load the data matrix into memory at once - + @@ -69,8 +69,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/singleCell_labels.html b/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/singleCell_labels.html index 51d214e5db..1212ff3658 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/singleCell_labels.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/singleCell_labels.html @@ -5,7 +5,7 @@ singleCell_labels - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/spatial_labels.html b/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/spatial_labels.html index 6f5b6ce07e..4c303cc7a8 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/spatial_labels.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/spatial_labels.html @@ -5,7 +5,7 @@ get the labels based on the spatial information of each spot - + @@ -72,8 +72,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/spot_vector.html b/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/spot_vector.html index b8c41c2778..098e7e50ac 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/spot_vector.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/spot_vector.html @@ -5,7 +5,7 @@ get the cell spot embedding result - + @@ -63,8 +63,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/total_peaksum.html b/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/total_peaksum.html index 91d38d8241..ff6f6e1861 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/total_peaksum.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/total_peaksum.html @@ -5,7 +5,7 @@ do matrix data normalization via total peak sum - + @@ -68,8 +68,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/write.matrix.html b/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/write.matrix.html index 4ddc6c4b71..c32d3ea7c1 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/write.matrix.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/SingleCells/write.matrix.html @@ -5,7 +5,7 @@ write the single cell ion feature data matrix - + @@ -74,8 +74,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/ThermoRaw/MSI_pixels.html b/Rscript/Library/mzkit_app/vignettes/mzkit/ThermoRaw/MSI_pixels.html index 9f182f2646..05509eb449 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/ThermoRaw/MSI_pixels.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/ThermoRaw/MSI_pixels.html @@ -5,7 +5,7 @@ MSI_pixels - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/ThermoRaw/events.html b/Rscript/Library/mzkit_app/vignettes/mzkit/ThermoRaw/events.html index 4f511a82f7..67d2453133 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/ThermoRaw/events.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/ThermoRaw/events.html @@ -5,7 +5,7 @@ events - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/ThermoRaw/load_MSI.html b/Rscript/Library/mzkit_app/vignettes/mzkit/ThermoRaw/load_MSI.html index ae0ec5f0da..5e68e9d295 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/ThermoRaw/load_MSI.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/ThermoRaw/load_MSI.html @@ -5,7 +5,7 @@ load_MSI - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/ThermoRaw/logs.html b/Rscript/Library/mzkit_app/vignettes/mzkit/ThermoRaw/logs.html index e91b9ad7dd..48c21aa575 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/ThermoRaw/logs.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/ThermoRaw/logs.html @@ -5,7 +5,7 @@ logs - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/ThermoRaw/open.raw.html b/Rscript/Library/mzkit_app/vignettes/mzkit/ThermoRaw/open.raw.html index 4af6d5cd31..0f60ef9012 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/ThermoRaw/open.raw.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/ThermoRaw/open.raw.html @@ -5,7 +5,7 @@ open a Thermo raw file - + @@ -63,8 +63,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/ThermoRaw/read.rawscan.html b/Rscript/Library/mzkit_app/vignettes/mzkit/ThermoRaw/read.rawscan.html index 77414a5f43..6287cc8b88 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/ThermoRaw/read.rawscan.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/ThermoRaw/read.rawscan.html @@ -5,7 +5,7 @@ read.rawscan - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/TissueMorphology/TissueData.html b/Rscript/Library/mzkit_app/vignettes/mzkit/TissueMorphology/TissueData.html index 3c9c87bb4f..e21da4beae 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/TissueMorphology/TissueData.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/TissueMorphology/TissueData.html @@ -5,7 +5,7 @@ create a collection of the tissue region dataset - + @@ -82,8 +82,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/TissueMorphology/UMAPsample.html b/Rscript/Library/mzkit_app/vignettes/mzkit/TissueMorphology/UMAPsample.html index d2e8eba3d2..11450f6997 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/TissueMorphology/UMAPsample.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/TissueMorphology/UMAPsample.html @@ -5,7 +5,7 @@ create a collection of the umap sample data - + @@ -84,8 +84,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/TissueMorphology/gridding.html b/Rscript/Library/mzkit_app/vignettes/mzkit/TissueMorphology/gridding.html index 19d058e22a..7e31a08f00 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/TissueMorphology/gridding.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/TissueMorphology/gridding.html @@ -5,7 +5,7 @@ create a spatial grid for the spatial spot data - + @@ -75,8 +75,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/TissueMorphology/intersect_layer.html b/Rscript/Library/mzkit_app/vignettes/mzkit/TissueMorphology/intersect_layer.html index d3c40106bf..69af361166 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/TissueMorphology/intersect_layer.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/TissueMorphology/intersect_layer.html @@ -5,7 +5,7 @@ extract the missing tissue pixels based on the ion layer data - + @@ -68,8 +68,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/TissueMorphology/loadTissue.html b/Rscript/Library/mzkit_app/vignettes/mzkit/TissueMorphology/loadTissue.html index 791ea1992e..8765e60218 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/TissueMorphology/loadTissue.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/TissueMorphology/loadTissue.html @@ -5,7 +5,7 @@ load tissue region polygon data - + @@ -74,8 +74,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/TissueMorphology/loadUMAP.html b/Rscript/Library/mzkit_app/vignettes/mzkit/TissueMorphology/loadUMAP.html index f236176c8e..f13a2812a2 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/TissueMorphology/loadUMAP.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/TissueMorphology/loadUMAP.html @@ -5,7 +5,7 @@ load UMAP data - + @@ -67,8 +67,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/TissueMorphology/read.spatialMapping.html b/Rscript/Library/mzkit_app/vignettes/mzkit/TissueMorphology/read.spatialMapping.html index eef78ce865..f63df438f8 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/TissueMorphology/read.spatialMapping.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/TissueMorphology/read.spatialMapping.html @@ -5,7 +5,7 @@ read spatial mapping data of STdata mapping to SMdata - + @@ -68,8 +68,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/TissueMorphology/splitMapping.html b/Rscript/Library/mzkit_app/vignettes/mzkit/TissueMorphology/splitMapping.html index 7c99b98ff4..74c4cccbf3 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/TissueMorphology/splitMapping.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/TissueMorphology/splitMapping.html @@ -5,7 +5,7 @@ Split the spatial mapping by tissue label data - + @@ -63,8 +63,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/TissueMorphology/tag_samples.html b/Rscript/Library/mzkit_app/vignettes/mzkit/TissueMorphology/tag_samples.html index 8085bcf218..d725eb6781 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/TissueMorphology/tag_samples.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/TissueMorphology/tag_samples.html @@ -5,7 +5,7 @@ Add tissue region label to the pixels of the ms-imaging data - + @@ -73,8 +73,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/TissueMorphology/writeCDF.html b/Rscript/Library/mzkit_app/vignettes/mzkit/TissueMorphology/writeCDF.html index f0b4375cb8..f72cd178bc 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/TissueMorphology/writeCDF.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/TissueMorphology/writeCDF.html @@ -5,7 +5,7 @@ export the tissue data as cdf file - + @@ -81,8 +81,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/UVSpectroscopy/as.UVtime_signals.html b/Rscript/Library/mzkit_app/vignettes/mzkit/UVSpectroscopy/as.UVtime_signals.html index fe9789936b..dd7a84ae82 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/UVSpectroscopy/as.UVtime_signals.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/UVSpectroscopy/as.UVtime_signals.html @@ -5,7 +5,7 @@ as.UVtime_signals - + @@ -61,8 +61,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/UVSpectroscopy/extract_UVsignals.html b/Rscript/Library/mzkit_app/vignettes/mzkit/UVSpectroscopy/extract_UVsignals.html index 428113da1e..078f787442 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/UVSpectroscopy/extract_UVsignals.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/UVSpectroscopy/extract_UVsignals.html @@ -5,7 +5,7 @@ extract_UVsignals - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/UVSpectroscopy/get_instrument.html b/Rscript/Library/mzkit_app/vignettes/mzkit/UVSpectroscopy/get_instrument.html index 211149b4d2..469b9dbe6f 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/UVSpectroscopy/get_instrument.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/UVSpectroscopy/get_instrument.html @@ -5,7 +5,7 @@ Get photodiode array detector instrument configuration id - + @@ -63,8 +63,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/UVSpectroscopy/read.UVsignals.html b/Rscript/Library/mzkit_app/vignettes/mzkit/UVSpectroscopy/read.UVsignals.html index e76fa65dee..1de3ec93b7 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/UVSpectroscopy/read.UVsignals.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/UVSpectroscopy/read.UVsignals.html @@ -5,7 +5,7 @@ - + @@ -67,8 +67,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/UVSpectroscopy/write.UVsignals.html b/Rscript/Library/mzkit_app/vignettes/mzkit/UVSpectroscopy/write.UVsignals.html index bf223c97cd..a72ff5783e 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/UVSpectroscopy/write.UVsignals.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/UVSpectroscopy/write.UVsignals.html @@ -5,7 +5,7 @@ write UV signal data into a text file or netCDF4 data file - + @@ -77,8 +77,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/assert.adducts.html b/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/assert.adducts.html index 7c03015492..a0d9321be3 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/assert.adducts.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/assert.adducts.html @@ -5,7 +5,7 @@ assert.adducts - + @@ -61,8 +61,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/checkInSourceFragments.html b/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/checkInSourceFragments.html index 228c6f4d2e..c59e5a469b 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/checkInSourceFragments.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/checkInSourceFragments.html @@ -5,7 +5,7 @@ Check the ms1 parent ion is generated via the in-source fragment or not - + @@ -76,8 +76,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/commit.html b/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/commit.html index f6e7c1e13a..10f487e5d2 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/commit.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/commit.html @@ -5,7 +5,7 @@ Commit library annotation - + @@ -67,8 +67,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/filter.html b/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/filter.html index 3cf9f1d044..dc23235737 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/filter.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/filter.html @@ -5,7 +5,7 @@ filter - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/get_annotations.html b/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/get_annotations.html index 4d3be0448b..e94249a852 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/get_annotations.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/get_annotations.html @@ -5,7 +5,7 @@ get annotation data from the given workspace object - + @@ -67,8 +67,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/get_peaktable.html b/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/get_peaktable.html index 211b688032..e32621f3b9 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/get_peaktable.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/get_peaktable.html @@ -5,7 +5,7 @@ get annotated ms1 peak features from the result data pack - + @@ -67,8 +67,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/make.annotation.html b/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/make.annotation.html index 021c40912a..f06880f566 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/make.annotation.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/make.annotation.html @@ -5,7 +5,7 @@ create a new metabolite annotation information - + @@ -81,8 +81,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/open.annotation_workspace.html b/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/open.annotation_workspace.html index 31fb4ac5f6..94cebb23a4 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/open.annotation_workspace.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/open.annotation_workspace.html @@ -5,7 +5,7 @@ - + @@ -73,8 +73,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/peak_assign.html b/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/peak_assign.html index 7c8180f734..9a25a7e0a0 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/peak_assign.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/peak_assign.html @@ -5,7 +5,7 @@ Associates the ms1 peaks with the ms2 spectrum alignment result hits. - + @@ -91,8 +91,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/populateIonData.html b/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/populateIonData.html index 9db116141a..8f0d1cef63 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/populateIonData.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/populateIonData.html @@ -5,7 +5,7 @@ a shortcut method for populate the peak ms2 data from a mzpack raw data file - + @@ -72,8 +72,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/push_temp.html b/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/push_temp.html index e9db42466b..6938011d1c 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/push_temp.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/push_temp.html @@ -5,7 +5,7 @@ Save the ms2 alignment hits result into current temp workspace. - + @@ -107,8 +107,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/read.annotationPack.html b/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/read.annotationPack.html index 3816db2dd0..3edee90d4a 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/read.annotationPack.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/read.annotationPack.html @@ -5,7 +5,7 @@ read.annotationPack - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/save_annotations.html b/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/save_annotations.html index 8e2bde928f..2fa93f25b4 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/save_annotations.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/save_annotations.html @@ -5,7 +5,7 @@ Save the reference library annotation result. - + @@ -71,8 +71,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/set_xicCache.html b/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/set_xicCache.html index bc2a5ba622..41c3fb0a4a 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/set_xicCache.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/set_xicCache.html @@ -5,7 +5,7 @@ - + @@ -82,8 +82,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/workspace.html b/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/workspace.html index dba3b6e552..dd185e9fa3 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/workspace.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/workspace.html @@ -5,7 +5,7 @@ create an empty workspace object - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/xref.html b/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/xref.html index 9f6ef47aeb..72be6cb3a4 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/xref.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/annotation/xref.html @@ -5,7 +5,7 @@ Create the database cross reference links - + @@ -406,8 +406,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/assembly/file.index.html b/Rscript/Library/mzkit_app/vignettes/mzkit/assembly/file.index.html index f8a7ec82bb..145d0b1f06 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/assembly/file.index.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/assembly/file.index.html @@ -5,7 +5,7 @@ get file index string of the given ms2 peak data. - + @@ -63,8 +63,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/assembly/load_index.html b/Rscript/Library/mzkit_app/vignettes/mzkit/assembly/load_index.html index a352d6628d..57cf7d8f96 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/assembly/load_index.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/assembly/load_index.html @@ -5,7 +5,7 @@ load_index - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/assembly/mgf.ion_peaks.html b/Rscript/Library/mzkit_app/vignettes/mzkit/assembly/mgf.ion_peaks.html index 9dbfd7cb57..bb38f439b3 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/assembly/mgf.ion_peaks.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/assembly/mgf.ion_peaks.html @@ -5,7 +5,7 @@ this function ensure that the output result of the any input ion objects is peakms2 data type. - + @@ -68,8 +68,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/assembly/ms1.scans.html b/Rscript/Library/mzkit_app/vignettes/mzkit/assembly/ms1.scans.html index 217976a4be..dddf5835cc 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/assembly/ms1.scans.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/assembly/ms1.scans.html @@ -5,7 +5,7 @@ get all ms1 raw scans from the raw files - + @@ -68,8 +68,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/assembly/mzxml.mgf.html b/Rscript/Library/mzkit_app/vignettes/mzkit/assembly/mzxml.mgf.html index 1b2509219b..c4fdf473fc 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/assembly/mzxml.mgf.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/assembly/mzxml.mgf.html @@ -5,7 +5,7 @@ Convert mzxml file as mgf ions. - + @@ -65,8 +65,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/assembly/open.xml_seek.html b/Rscript/Library/mzkit_app/vignettes/mzkit/assembly/open.xml_seek.html index 0979ec071f..3edc73364e 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/assembly/open.xml_seek.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/assembly/open.xml_seek.html @@ -5,7 +5,7 @@ open.xml_seek - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/assembly/polarity.html b/Rscript/Library/mzkit_app/vignettes/mzkit/assembly/polarity.html index bf25a32526..f2ea82edcd 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/assembly/polarity.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/assembly/polarity.html @@ -5,7 +5,7 @@ get polarity data for each ms2 scans - + @@ -67,8 +67,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/assembly/raw.scans.html b/Rscript/Library/mzkit_app/vignettes/mzkit/assembly/raw.scans.html index 7e1485e812..f999e432f9 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/assembly/raw.scans.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/assembly/raw.scans.html @@ -5,7 +5,7 @@ get raw scans data from the ``mzXML`` or ``mzMl`` data file - + @@ -67,8 +67,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/assembly/read.mgf.html b/Rscript/Library/mzkit_app/vignettes/mzkit/assembly/read.mgf.html index cdb2eb0cda..cbb4829c81 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/assembly/read.mgf.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/assembly/read.mgf.html @@ -5,7 +5,7 @@ Read the spectrum data inside a mgf ASCII data file. - + @@ -63,8 +63,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/assembly/read.msl.html b/Rscript/Library/mzkit_app/vignettes/mzkit/assembly/read.msl.html index 3e057209ed..7e165bc491 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/assembly/read.msl.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/assembly/read.msl.html @@ -5,7 +5,7 @@ read MSL data files - + @@ -68,8 +68,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/assembly/read.msp.html b/Rscript/Library/mzkit_app/vignettes/mzkit/assembly/read.msp.html index 2d77a5de90..c617d96cce 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/assembly/read.msp.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/assembly/read.msp.html @@ -5,7 +5,7 @@ - + @@ -68,8 +68,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/assembly/scan_id.html b/Rscript/Library/mzkit_app/vignettes/mzkit/assembly/scan_id.html index 11c5a7a3d2..b12fdf5480 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/assembly/scan_id.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/assembly/scan_id.html @@ -5,7 +5,7 @@ get all scan id from the ms xml file - + @@ -63,8 +63,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/assembly/seek.html b/Rscript/Library/mzkit_app/vignettes/mzkit/assembly/seek.html index 204b86d563..1e45f1fcad 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/assembly/seek.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/assembly/seek.html @@ -5,7 +5,7 @@ seek - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/assembly/write.mgf.html b/Rscript/Library/mzkit_app/vignettes/mzkit/assembly/write.mgf.html index 601824bbb1..29cae7c5c7 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/assembly/write.mgf.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/assembly/write.mgf.html @@ -5,7 +5,7 @@ write spectra data in mgf file format. - + @@ -73,8 +73,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/cellsPack/pack_cells.group.html b/Rscript/Library/mzkit_app/vignettes/mzkit/cellsPack/pack_cells.group.html index 71af18f995..5e02596757 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/cellsPack/pack_cells.group.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/cellsPack/pack_cells.group.html @@ -5,7 +5,7 @@ pack of the single cells metabolomics data in multiple sample groups - + @@ -89,8 +89,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/cellsPack/pack_cells.html b/Rscript/Library/mzkit_app/vignettes/mzkit/cellsPack/pack_cells.html index 13420cac11..380bf14746 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/cellsPack/pack_cells.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/cellsPack/pack_cells.html @@ -5,7 +5,7 @@ pack of the multiple raw data files into one data pack - + @@ -74,8 +74,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/chromatogram/as.chromatogram.html b/Rscript/Library/mzkit_app/vignettes/mzkit/chromatogram/as.chromatogram.html index ed80d6c6d1..8ccbf0c099 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/chromatogram/as.chromatogram.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/chromatogram/as.chromatogram.html @@ -5,7 +5,7 @@ convert dataset to chromatography dataset - + @@ -79,8 +79,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/chromatogram/labels.html b/Rscript/Library/mzkit_app/vignettes/mzkit/chromatogram/labels.html index a0b6f687c5..398ca4a2d0 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/chromatogram/labels.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/chromatogram/labels.html @@ -5,7 +5,7 @@ set new labels to the chromatogram overlap data - + @@ -71,8 +71,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/chromatogram/overlaps.html b/Rscript/Library/mzkit_app/vignettes/mzkit/chromatogram/overlaps.html index 8e61bd7d22..624b72ebe0 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/chromatogram/overlaps.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/chromatogram/overlaps.html @@ -5,7 +5,7 @@ Create chromatogram overlaps from a set of chromatogram objects - + @@ -71,8 +71,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/chromatogram/overlapsMatrix.html b/Rscript/Library/mzkit_app/vignettes/mzkit/chromatogram/overlapsMatrix.html index 604cef0cd0..b44fe0493c 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/chromatogram/overlapsMatrix.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/chromatogram/overlapsMatrix.html @@ -5,7 +5,7 @@ Convert the overlap list to the matrix - + @@ -68,8 +68,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/chromatogram/read.pack.html b/Rscript/Library/mzkit_app/vignettes/mzkit/chromatogram/read.pack.html index 88312e4df4..39b35a9bb7 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/chromatogram/read.pack.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/chromatogram/read.pack.html @@ -5,7 +5,7 @@ read.pack - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/chromatogram/scale_time.html b/Rscript/Library/mzkit_app/vignettes/mzkit/chromatogram/scale_time.html index 7d706dd3a0..c467ddfeff 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/chromatogram/scale_time.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/chromatogram/scale_time.html @@ -5,7 +5,7 @@ scale the RT into different time data unit - + @@ -68,8 +68,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/chromatogram/subset.html b/Rscript/Library/mzkit_app/vignettes/mzkit/chromatogram/subset.html index 84c5b8bef7..cdf3453d05 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/chromatogram/subset.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/chromatogram/subset.html @@ -5,7 +5,7 @@ get subset of the chromatogram data by names - + @@ -67,8 +67,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/chromatogram/toChromatogram.html b/Rscript/Library/mzkit_app/vignettes/mzkit/chromatogram/toChromatogram.html index aa57b6b42b..354f8ce4c1 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/chromatogram/toChromatogram.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/chromatogram/toChromatogram.html @@ -5,7 +5,7 @@ Convert chromatogram tick point data to a chromatogram object - + @@ -73,8 +73,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/chromatogram/topInto.html b/Rscript/Library/mzkit_app/vignettes/mzkit/chromatogram/topInto.html index 58191755fa..d3957fc349 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/chromatogram/topInto.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/chromatogram/topInto.html @@ -5,7 +5,7 @@ topInto - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/chromatogram/write.pack.html b/Rscript/Library/mzkit_app/vignettes/mzkit/chromatogram/write.pack.html index 6b4daf9a38..35c22c3983 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/chromatogram/write.pack.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/chromatogram/write.pack.html @@ -5,7 +5,7 @@ save the chrome overlaps data as the cdf data file - + @@ -67,8 +67,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/data/XIC.html b/Rscript/Library/mzkit_app/vignettes/mzkit/data/XIC.html index e42d5f8428..8c5ab7bd38 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/data/XIC.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/data/XIC.html @@ -5,7 +5,7 @@ get chromatogram data for a specific metabolite with given m/z from the ms1 scans data. - + @@ -78,8 +78,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/data/XIC_groups.html b/Rscript/Library/mzkit_app/vignettes/mzkit/data/XIC_groups.html index feaf30d8ed..49ed97755f 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/data/XIC_groups.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/data/XIC_groups.html @@ -5,7 +5,7 @@ grouping of the ms1 scan points by m/z data - + @@ -73,8 +73,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/data/groupBy_ROI.html b/Rscript/Library/mzkit_app/vignettes/mzkit/data/groupBy_ROI.html index f3dc3bf0f7..5f978c2683 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/data/groupBy_ROI.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/data/groupBy_ROI.html @@ -5,7 +5,7 @@ make a tuple list via grouping of the spectrum data via the ROI id inside the metadata list - + @@ -73,8 +73,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/data/intensity.html b/Rscript/Library/mzkit_app/vignettes/mzkit/data/intensity.html index a72226fbbb..2d9fb1c91b 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/data/intensity.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/data/intensity.html @@ -5,7 +5,7 @@ get intensity value from the ion scan points - + @@ -69,8 +69,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/data/libraryMatrix.html b/Rscript/Library/mzkit_app/vignettes/mzkit/data/libraryMatrix.html index b26cdaced8..e27f7b21a3 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/data/libraryMatrix.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/data/libraryMatrix.html @@ -5,7 +5,7 @@ Create a library matrix object - + @@ -81,8 +81,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/data/linearMatrix.html b/Rscript/Library/mzkit_app/vignettes/mzkit/data/linearMatrix.html index a2815dc688..278cdb22d4 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/data/linearMatrix.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/data/linearMatrix.html @@ -5,7 +5,7 @@ linearMatrix - + @@ -61,8 +61,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/data/make.ROI_names.html b/Rscript/Library/mzkit_app/vignettes/mzkit/data/make.ROI_names.html index 59a7274043..acc3622670 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/data/make.ROI_names.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/data/make.ROI_names.html @@ -5,7 +5,7 @@ makes xcms_id format liked ROI unique id - + @@ -73,8 +73,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/data/nsize.html b/Rscript/Library/mzkit_app/vignettes/mzkit/data/nsize.html index 611cf12239..a312b8925a 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/data/nsize.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/data/nsize.html @@ -5,7 +5,7 @@ get the size of the target ms peaks - + @@ -63,8 +63,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/data/peakMs2.html b/Rscript/Library/mzkit_app/vignettes/mzkit/data/peakMs2.html index 125c0431af..32249a54ac 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/data/peakMs2.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/data/peakMs2.html @@ -5,7 +5,7 @@ create a new ms2 peaks data object - + @@ -96,8 +96,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/data/read.MsMatrix.html b/Rscript/Library/mzkit_app/vignettes/mzkit/data/read.MsMatrix.html index 54c77a6426..b841682e03 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/data/read.MsMatrix.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/data/read.MsMatrix.html @@ -5,7 +5,7 @@ read.MsMatrix - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/data/representative.html b/Rscript/Library/mzkit_app/vignettes/mzkit/data/representative.html index 57bd147f49..4836c40ec9 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/data/representative.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/data/representative.html @@ -5,7 +5,7 @@ Create a representative spectrum from a given spectrum collection via a sum or mean aggregate method. - + @@ -70,8 +70,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/data/rt_slice.html b/Rscript/Library/mzkit_app/vignettes/mzkit/data/rt_slice.html index c48579c41a..d2d6cbdbd9 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/data/rt_slice.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/data/rt_slice.html @@ -5,7 +5,7 @@ slice a region of ms1 scan data by a given rt window. - + @@ -75,8 +75,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/data/scan_time.html b/Rscript/Library/mzkit_app/vignettes/mzkit/data/scan_time.html index a5f3ae429e..e9795aa857 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/data/scan_time.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/data/scan_time.html @@ -5,7 +5,7 @@ get scan time value from the ion scan points - + @@ -67,8 +67,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/data/search.html b/Rscript/Library/mzkit_app/vignettes/mzkit/data/search.html index 46814ca021..76490917fa 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/data/search.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/data/search.html @@ -5,7 +5,7 @@ search the target query spectra against a reference mzpack data file - + @@ -73,8 +73,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/data/splash_id.html b/Rscript/Library/mzkit_app/vignettes/mzkit/data/splash_id.html index 0eab7a3db1..78096aaae3 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/data/splash_id.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/data/splash_id.html @@ -5,7 +5,7 @@ evaluate the splash id of the given spectrum data - + @@ -81,8 +81,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/data/unionPeaks.html b/Rscript/Library/mzkit_app/vignettes/mzkit/data/unionPeaks.html index 6aebe23d2d..5a5d3a2982 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/data/unionPeaks.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/data/unionPeaks.html @@ -5,7 +5,7 @@ Union and merge the given multiple spectrum data into one single spectrum - + @@ -76,8 +76,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/flexImaging/importSpotList.html b/Rscript/Library/mzkit_app/vignettes/mzkit/flexImaging/importSpotList.html index 624d096ecf..7ef0e35a75 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/flexImaging/importSpotList.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/flexImaging/importSpotList.html @@ -5,7 +5,7 @@ importSpotList - + @@ -61,8 +61,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/flexImaging/importsExperiment.html b/Rscript/Library/mzkit_app/vignettes/mzkit/flexImaging/importsExperiment.html index 3924e22f4d..d304b0c061 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/flexImaging/importsExperiment.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/flexImaging/importsExperiment.html @@ -5,7 +5,7 @@ importsExperiment - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/flexImaging/read.metadata.html b/Rscript/Library/mzkit_app/vignettes/mzkit/flexImaging/read.metadata.html index 1d92bf4723..6a510b8e1f 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/flexImaging/read.metadata.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/flexImaging/read.metadata.html @@ -5,7 +5,7 @@ read.metadata - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/foodb/loadFoods.html b/Rscript/Library/mzkit_app/vignettes/mzkit/foodb/loadFoods.html index 4391835974..1356505d4d 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/foodb/loadFoods.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/foodb/loadFoods.html @@ -5,7 +5,7 @@ Load foodb database csv dump - + @@ -67,8 +67,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/formula/KCF.graph.html b/Rscript/Library/mzkit_app/vignettes/mzkit/formula/KCF.graph.html index 7222377466..260ac49633 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/formula/KCF.graph.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/formula/KCF.graph.html @@ -5,7 +5,7 @@ Create molecular network graph model - + @@ -63,8 +63,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/formula/SDF.convertKCF.html b/Rscript/Library/mzkit_app/vignettes/mzkit/formula/SDF.convertKCF.html index 708eeda977..d701f8f7ef 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/formula/SDF.convertKCF.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/formula/SDF.convertKCF.html @@ -5,7 +5,7 @@ SDF.convertKCF - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/formula/candidates.html b/Rscript/Library/mzkit_app/vignettes/mzkit/formula/candidates.html index 62107a2aa8..7640a32f98 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/formula/candidates.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/formula/candidates.html @@ -5,7 +5,7 @@ find all of the candidate chemical formulas by a - + @@ -73,8 +73,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/formula/canonical_formula.html b/Rscript/Library/mzkit_app/vignettes/mzkit/formula/canonical_formula.html index 5692708686..e3482f9160 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/formula/canonical_formula.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/formula/canonical_formula.html @@ -5,7 +5,7 @@ Make the given formula string into canonical format - + @@ -67,8 +67,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/formula/descriptor.matrix.html b/Rscript/Library/mzkit_app/vignettes/mzkit/formula/descriptor.matrix.html index bb516f9ee3..ad5c5e43c2 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/formula/descriptor.matrix.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/formula/descriptor.matrix.html @@ -5,7 +5,7 @@ descriptor.matrix - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/formula/eval.html b/Rscript/Library/mzkit_app/vignettes/mzkit/formula/eval.html index fdff22b9cd..845d2d0607 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/formula/eval.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/formula/eval.html @@ -5,7 +5,7 @@ Evaluate formula exact mass - + @@ -67,8 +67,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/formula/formula_calibration.html b/Rscript/Library/mzkit_app/vignettes/mzkit/formula/formula_calibration.html index 8570a9b57c..1c16137f21 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/formula/formula_calibration.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/formula/formula_calibration.html @@ -5,7 +5,7 @@ formula_calibration - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/formula/getElementCount.html b/Rscript/Library/mzkit_app/vignettes/mzkit/formula/getElementCount.html index ba43e15111..b039a94d0c 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/formula/getElementCount.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/formula/getElementCount.html @@ -5,7 +5,7 @@ getElementCount - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/formula/isotope_distribution.html b/Rscript/Library/mzkit_app/vignettes/mzkit/formula/isotope_distribution.html index 66903c65ef..8840be7d26 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/formula/isotope_distribution.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/formula/isotope_distribution.html @@ -5,7 +5,7 @@ isotope_distribution - + @@ -65,8 +65,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/formula/open.descriptor.db.html b/Rscript/Library/mzkit_app/vignettes/mzkit/formula/open.descriptor.db.html index 2d574ebae2..6b33612bd9 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/formula/open.descriptor.db.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/formula/open.descriptor.db.html @@ -5,7 +5,7 @@ open the file handles of the chemical descriptor database. - + @@ -64,8 +64,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/formula/parse.SDF.html b/Rscript/Library/mzkit_app/vignettes/mzkit/formula/parse.SDF.html index 50bb89c8c2..d1ca873ca0 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/formula/parse.SDF.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/formula/parse.SDF.html @@ -5,7 +5,7 @@ parse a single sdf text block - + @@ -68,8 +68,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/formula/peaks_annotation.html b/Rscript/Library/mzkit_app/vignettes/mzkit/formula/peaks_annotation.html index bfb3e69d6c..922e598718 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/formula/peaks_annotation.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/formula/peaks_annotation.html @@ -5,7 +5,7 @@ do peak annotation for the ms2 spectrum fragments - + @@ -80,8 +80,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/formula/read.KCF.html b/Rscript/Library/mzkit_app/vignettes/mzkit/formula/read.KCF.html index 6b846cdea5..fb2b051c8e 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/formula/read.KCF.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/formula/read.KCF.html @@ -5,7 +5,7 @@ Read KCF model data - + @@ -63,8 +63,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/formula/registerAnnotations.html b/Rscript/Library/mzkit_app/vignettes/mzkit/formula/registerAnnotations.html index a24710f4c3..1b87c564f7 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/formula/registerAnnotations.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/formula/registerAnnotations.html @@ -5,7 +5,7 @@ registerAnnotations - + @@ -61,8 +61,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/formula/removeElement.html b/Rscript/Library/mzkit_app/vignettes/mzkit/formula/removeElement.html index 8ce3a8ef12..4b06cbbac9 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/formula/removeElement.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/formula/removeElement.html @@ -5,7 +5,7 @@ removeElement - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/formula/scan.html b/Rscript/Library/mzkit_app/vignettes/mzkit/formula/scan.html index 8fed1618ae..86488af125 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/formula/scan.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/formula/scan.html @@ -5,7 +5,7 @@ Get atom composition from a formula string - + @@ -63,8 +63,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/hmdb_kit/biospecimen_slicer.html b/Rscript/Library/mzkit_app/vignettes/mzkit/hmdb_kit/biospecimen_slicer.html index bdb7dff10d..d819718991 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/hmdb_kit/biospecimen_slicer.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/hmdb_kit/biospecimen_slicer.html @@ -5,7 +5,7 @@ split the hmdb database by biospecimen locations - + @@ -71,8 +71,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/hmdb_kit/chemical_taxonomy.html b/Rscript/Library/mzkit_app/vignettes/mzkit/hmdb_kit/chemical_taxonomy.html index 08a62d207c..f1004fcdcf 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/hmdb_kit/chemical_taxonomy.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/hmdb_kit/chemical_taxonomy.html @@ -5,7 +5,7 @@ Extract the chemical taxonomy data - + @@ -63,8 +63,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/hmdb_kit/export.hmdb_table.html b/Rscript/Library/mzkit_app/vignettes/mzkit/hmdb_kit/export.hmdb_table.html index 7b2bbe79fd..725d84744e 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/hmdb_kit/export.hmdb_table.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/hmdb_kit/export.hmdb_table.html @@ -5,7 +5,7 @@ save the hmdb database as a csv table file - + @@ -73,8 +73,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/hmdb_kit/get_hmdb.html b/Rscript/Library/mzkit_app/vignettes/mzkit/hmdb_kit/get_hmdb.html index 08c0659b92..f433e1e095 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/hmdb_kit/get_hmdb.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/hmdb_kit/get_hmdb.html @@ -5,7 +5,7 @@ get metabolite via a given hmdb id from the hmdb.ca online web services - + @@ -65,8 +65,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/hmdb_kit/read.hmdb.html b/Rscript/Library/mzkit_app/vignettes/mzkit/hmdb_kit/read.hmdb.html index 33ed04a0fa..5ba94e3c94 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/hmdb_kit/read.hmdb.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/hmdb_kit/read.hmdb.html @@ -5,7 +5,7 @@ open a reader for read hmdb database - + @@ -64,8 +64,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/hmdb_kit/read.hmdb_spectrals.html b/Rscript/Library/mzkit_app/vignettes/mzkit/hmdb_kit/read.hmdb_spectrals.html index 093d8aa8d2..c2fb1bd418 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/hmdb_kit/read.hmdb_spectrals.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/hmdb_kit/read.hmdb_spectrals.html @@ -5,7 +5,7 @@ read hmdb spectral data collection - + @@ -77,8 +77,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/as.lipidmaps.html b/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/as.lipidmaps.html index 7ecd0a6283..44a17a246e 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/as.lipidmaps.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/as.lipidmaps.html @@ -5,7 +5,7 @@ populate lipidmaps meta data objects from the loaded sdf data stream - + @@ -71,8 +71,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/chebi.secondary2main.mapping.html b/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/chebi.secondary2main.mapping.html index 559e4f712a..68fe2baa18 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/chebi.secondary2main.mapping.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/chebi.secondary2main.mapping.html @@ -5,7 +5,7 @@ chebi.secondary2main.mapping - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/extract_chebi_compounds.html b/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/extract_chebi_compounds.html index a0a1ca8b7b..6983e3d69a 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/extract_chebi_compounds.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/extract_chebi_compounds.html @@ -5,7 +5,7 @@ extract the chebi annotation data from the chebi ontology data - + @@ -63,8 +63,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/glycosyl.solver.html b/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/glycosyl.solver.html index 2ebffd629c..b60f43b894 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/glycosyl.solver.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/glycosyl.solver.html @@ -5,7 +5,7 @@ glycosyl.solver - + @@ -61,8 +61,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/glycosyl.tokens.html b/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/glycosyl.tokens.html index f2e0c97e12..3d20080668 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/glycosyl.tokens.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/glycosyl.tokens.html @@ -5,7 +5,7 @@ glycosyl.tokens - + @@ -61,8 +61,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/hmdb.secondary2main.mapping.html b/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/hmdb.secondary2main.mapping.html index a382f84359..44d463af5e 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/hmdb.secondary2main.mapping.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/hmdb.secondary2main.mapping.html @@ -5,7 +5,7 @@ hmdb.secondary2main.mapping - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/inchikey.html b/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/inchikey.html index 8cbadd514e..8e1271dc3f 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/inchikey.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/inchikey.html @@ -5,7 +5,7 @@ generates the inchikey hashcode based on the given inchi data - + @@ -67,8 +67,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/lipid.class.html b/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/lipid.class.html index e12ed83f73..c557f8ab4b 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/lipid.class.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/lipid.class.html @@ -5,7 +5,7 @@ Create lipid class helper for annotation - + @@ -73,8 +73,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/lipid.nameMaps.html b/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/lipid.nameMaps.html index 28936cb33f..ff8fdea938 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/lipid.nameMaps.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/lipid.nameMaps.html @@ -5,7 +5,7 @@ lipid.nameMaps - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/lipid.names.html b/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/lipid.names.html index 7161547a15..db89dfd097 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/lipid.names.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/lipid.names.html @@ -5,7 +5,7 @@ Create lipid name helper for annotation - + @@ -72,8 +72,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/lipid_classprofiles.html b/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/lipid_classprofiles.html index ce23a17b3a..009e7d9eee 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/lipid_classprofiles.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/lipid_classprofiles.html @@ -5,7 +5,7 @@ lipid_classprofiles - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/lipid_profiles.html b/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/lipid_profiles.html index 48fa551900..4b79b05ee7 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/lipid_profiles.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/lipid_profiles.html @@ -5,7 +5,7 @@ lipid_profiles - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/lipidmaps_id.html b/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/lipidmaps_id.html index bc60e93374..9c47a2ea7d 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/lipidmaps_id.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/lipidmaps_id.html @@ -5,7 +5,7 @@ gets the metabolite id collection from lipidmaps database - + @@ -67,8 +67,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/metabo_anno.html b/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/metabo_anno.html index c3e75b382f..3a62c37cb4 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/metabo_anno.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/metabo_anno.html @@ -5,7 +5,7 @@ construct a new metabolite annotation information data - + @@ -87,8 +87,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/mona.msp_metadata.html b/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/mona.msp_metadata.html index 7ffd831585..e6dbf1e648 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/mona.msp_metadata.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/mona.msp_metadata.html @@ -5,7 +5,7 @@ Extract the annotation metadata from the MONA comment data - + @@ -63,8 +63,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/parse.ChEBI_entity.html b/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/parse.ChEBI_entity.html index 87d9982fa6..25618b64f0 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/parse.ChEBI_entity.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/parse.ChEBI_entity.html @@ -5,7 +5,7 @@ parse.ChEBI_entity - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/rankingNames.html b/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/rankingNames.html index 1cb93f8e06..262750b832 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/rankingNames.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/rankingNames.html @@ -5,7 +5,7 @@ Ranking a set of the given synonym string collection for find common name. - + @@ -73,8 +73,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/read.MoNA.html b/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/read.MoNA.html index 39b8579fe8..6c3c020656 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/read.MoNA.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/read.MoNA.html @@ -5,7 +5,7 @@ read MoNA database file. - + @@ -74,8 +74,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/read.RefMet.html b/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/read.RefMet.html index 48489c07ac..69e18cd417 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/read.RefMet.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/read.RefMet.html @@ -5,7 +5,7 @@ read the csv table of refmet - + @@ -66,8 +66,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/read.SDF.html b/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/read.SDF.html index 692e1c7886..11812fba66 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/read.SDF.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/read.SDF.html @@ -5,7 +5,7 @@ read metabolite data in a given sdf data file. - + @@ -73,8 +73,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/read.lipidmaps.html b/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/read.lipidmaps.html index 2323af24a1..3eab5afd02 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/read.lipidmaps.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/read.lipidmaps.html @@ -5,7 +5,7 @@ read lipidmaps messagepack repository file - + @@ -78,8 +78,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/read.lotus.html b/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/read.lotus.html index 18b932338b..095be4d34c 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/read.lotus.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/read.lotus.html @@ -5,7 +5,7 @@ load the lotus natural products metabolite library from a given file - + @@ -68,8 +68,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/save.mapping.html b/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/save.mapping.html index e11d4e1193..edfbe7b9f2 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/save.mapping.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/save.mapping.html @@ -5,7 +5,7 @@ Save id mapping file in json file format - + @@ -71,8 +71,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/secondary2main.mapping.html b/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/secondary2main.mapping.html index 49aab4aea2..a5bc87d827 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/secondary2main.mapping.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/secondary2main.mapping.html @@ -5,7 +5,7 @@ Create SecondaryIDSolver object from mapping file or mapping dictionary object data. - + @@ -63,8 +63,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/write.lipidmaps.html b/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/write.lipidmaps.html index 1fccb2afcc..43dbf621dd 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/write.lipidmaps.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/write.lipidmaps.html @@ -5,7 +5,7 @@ save lipidmaps data repository. - + @@ -71,8 +71,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/write.metalib.html b/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/write.metalib.html index 692d84837e..acf35de745 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/write.metalib.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/massbank/write.metalib.html @@ -5,7 +5,7 @@ write the metabolite annotation data collection as messagepack - + @@ -71,8 +71,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/math.html b/Rscript/Library/mzkit_app/vignettes/mzkit/math.html index 7128c2a313..c4f165759a 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/math.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/math.html @@ -79,7 +79,7 @@

math

spectrum_alignment: AlignmentOutput - +

the spectrum similarity comparision result object

diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/math/centroid.html b/Rscript/Library/mzkit_app/vignettes/mzkit/math/centroid.html index 13ad1a48a1..ee26ac0e9b 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/math/centroid.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/math/centroid.html @@ -5,7 +5,7 @@ Converts profiles peak data to peak data in centroid mode. - + @@ -91,8 +91,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/math/cluster.nodes.html b/Rscript/Library/mzkit_app/vignettes/mzkit/math/cluster.nodes.html index d5ed7afe14..cf5c9a5123 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/math/cluster.nodes.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/math/cluster.nodes.html @@ -5,7 +5,7 @@ get all nodes from the spectrum tree cluster result - + @@ -63,8 +63,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/math/cosine.html b/Rscript/Library/mzkit_app/vignettes/mzkit/math/cosine.html index 555cac596f..4a779442a2 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/math/cosine.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/math/cosine.html @@ -5,7 +5,7 @@ Do evaluate the spectra cosine similarity score - + @@ -58,9 +58,9 @@

Arguments

-

Details

+

Details

- +

this function andalso produce the jaccard/entropy similarity of the spectrum inside the similarity result object

Authors

@@ -70,9 +70,45 @@

Value

this function returns data object of type AlignmentOutput.

clr value class

-

Examples

- - +

Examples

+ +
 # create the spectrum matrix object
+ # fragment data tagged with the source name title
+ let spec1 = libraryMatrix(
+     matrix = data.frame(
+         mz = c(169.071, 186.066, 186.0769),
+         intensity = c(7.917962, 1.021589, 100.0)
+     ),
+     title = "Demo MS1 Spectra",
+     centroid = TRUE
+ );
+ let spec2 = libraryMatrix(
+     matrix = data.frame(
+         mz = c(120.212, 169.071, 186.066),
+         intensity = c(37.16, 66.83, 999.0)
+     ),
+     title = "Demo MS1 Spectra",
+     centroid = TRUE
+ );
+ let compares = math::cosine(spec1, spec2);
+ let scores = as.data.frame(compares, scores_df = TRUE);
+
+ print(scores);
+ #               dimension    scores 
+ # ----------------------------------
+ #            
+ # [1, ]  "forward cosine"  0.999925
+ # [2, ]  "reverse cosine"  0.999925
+ # [3, ]          "cosine"  0.999925
+ # [4, ]         "jaccard"         1
+ # [5, ]         "entropy"  0.999949
+ # [6, ]          "mirror"         1
+ # [7, ]            "mean"   0.99995
+ # [8, ]   "fragment hits"         2
+
+ svg(file = "figures/00_Mass_spectrometry/Math/03_compares.svg") {
+     plot(compares);
+ }

[Package math version 1.0.0.0 Examples
- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/math/cosine.pairwise.html b/Rscript/Library/mzkit_app/vignettes/mzkit/math/cosine.pairwise.html index f152fc56d2..070c0dec2d 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/math/cosine.pairwise.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/math/cosine.pairwise.html @@ -5,7 +5,7 @@ pairwise alignment of the spectrum peak set - + @@ -81,8 +81,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/math/defaultPrecursors.html b/Rscript/Library/mzkit_app/vignettes/mzkit/math/defaultPrecursors.html index 5af4711875..a56b600be7 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/math/defaultPrecursors.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/math/defaultPrecursors.html @@ -5,7 +5,7 @@ returns all precursor types for a given libtype - + @@ -63,8 +63,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/math/exact_mass.html b/Rscript/Library/mzkit_app/vignettes/mzkit/math/exact_mass.html index d1907ca19a..0b139ff3c5 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/math/exact_mass.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/math/exact_mass.html @@ -5,7 +5,7 @@ evaluate all exact mass for all known precursor type. - + @@ -72,8 +72,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/math/find_precursor.html b/Rscript/Library/mzkit_app/vignettes/mzkit/math/find_precursor.html index 92973fe672..1816248eac 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/math/find_precursor.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/math/find_precursor.html @@ -5,7 +5,7 @@ find precursor adducts type for a given mass and the corresponding precursor mz - + @@ -87,8 +87,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/math/intensity_vec.html b/Rscript/Library/mzkit_app/vignettes/mzkit/math/intensity_vec.html index 44a3f7f881..68481cf970 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/math/intensity_vec.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/math/intensity_vec.html @@ -5,7 +5,7 @@ Extract an intensity vector based on a given peak index - + @@ -75,8 +75,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/math/ions.unique.html b/Rscript/Library/mzkit_app/vignettes/mzkit/math/ions.unique.html index 2cbe4c197c..11d6adf219 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/math/ions.unique.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/math/ions.unique.html @@ -5,7 +5,7 @@ data pre-processing helper, make the spectra ion data unique - + @@ -102,8 +102,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/math/jaccard.html b/Rscript/Library/mzkit_app/vignettes/mzkit/math/jaccard.html index 302dff398f..0107d37d6b 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/math/jaccard.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/math/jaccard.html @@ -5,7 +5,7 @@ jaccard - + @@ -61,8 +61,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/math/jaccardSet.html b/Rscript/Library/mzkit_app/vignettes/mzkit/math/jaccardSet.html index 9b4daba2a7..c942f1e5e1 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/math/jaccardSet.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/math/jaccardSet.html @@ -5,7 +5,7 @@ search spectrum via the jaccard index method - + @@ -76,8 +76,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/math/mz.html b/Rscript/Library/mzkit_app/vignettes/mzkit/math/mz.html index 3d77985204..82ad604f11 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/math/mz.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/math/mz.html @@ -5,7 +5,7 @@ evaluate all m/z for all known precursor type. - + @@ -74,8 +74,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/math/mz_index.html b/Rscript/Library/mzkit_app/vignettes/mzkit/math/mz_index.html index 4c87725c30..d20b84afdc 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/math/mz_index.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/math/mz_index.html @@ -5,7 +5,7 @@ Create a peak index - + @@ -64,8 +64,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/math/norm_msdata.html b/Rscript/Library/mzkit_app/vignettes/mzkit/math/norm_msdata.html index 6890529b73..0fca7a4c6b 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/math/norm_msdata.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/math/norm_msdata.html @@ -5,7 +5,7 @@ normalized the peak intensity data, do [0,1] scaled. - + @@ -77,8 +77,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/math/ppm.html b/Rscript/Library/mzkit_app/vignettes/mzkit/math/ppm.html index 88ac606d7f..326e907ec7 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/math/ppm.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/math/ppm.html @@ -5,7 +5,7 @@ calculate ppm value between two mass vector - + @@ -67,8 +67,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/math/precursor_types.html b/Rscript/Library/mzkit_app/vignettes/mzkit/math/precursor_types.html index 56ed72fadb..0615807770 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/math/precursor_types.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/math/precursor_types.html @@ -5,7 +5,7 @@ create precursor type calculator - + @@ -75,8 +75,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/math/sequenceOrder.html b/Rscript/Library/mzkit_app/vignettes/mzkit/math/sequenceOrder.html index 156232f344..4e0f08d35f 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/math/sequenceOrder.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/math/sequenceOrder.html @@ -5,7 +5,7 @@ reorder scan points into a sequence for downstream data analysis - + @@ -77,8 +77,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/math/spectral_entropy.html b/Rscript/Library/mzkit_app/vignettes/mzkit/math/spectral_entropy.html index 266f445208..a1340fd977 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/math/spectral_entropy.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/math/spectral_entropy.html @@ -5,7 +5,7 @@ Search spectra with entropy similarity - + @@ -91,8 +91,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/math/spectrum.compares.html b/Rscript/Library/mzkit_app/vignettes/mzkit/math/spectrum.compares.html index 6f323f87c8..c25d2c889f 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/math/spectrum.compares.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/math/spectrum.compares.html @@ -5,7 +5,7 @@ create a delegate function pointer that apply for compares spectrums theirs similarity. - + @@ -80,8 +80,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/math/spectrum_tree.cluster.html b/Rscript/Library/mzkit_app/vignettes/mzkit/math/spectrum_tree.cluster.html index a8c92c1b8c..56c2489e9a 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/math/spectrum_tree.cluster.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/math/spectrum_tree.cluster.html @@ -5,7 +5,7 @@ create spectrum tree cluster based on the spectrum to spectrum similarity comparison. - + @@ -87,8 +87,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/math/toMS.html b/Rscript/Library/mzkit_app/vignettes/mzkit/math/toMS.html index 7973addb5e..4cc84e247e 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/math/toMS.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/math/toMS.html @@ -5,7 +5,7 @@ toMS - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/math/tolerance.html b/Rscript/Library/mzkit_app/vignettes/mzkit/math/tolerance.html index 93ac71827d..2906b814bd 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/math/tolerance.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/math/tolerance.html @@ -5,7 +5,7 @@ Create tolerance object - + @@ -69,8 +69,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/math/xcms_id.html b/Rscript/Library/mzkit_app/vignettes/mzkit/math/xcms_id.html index 11b85a16f3..6ce4093369 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/math/xcms_id.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/math/xcms_id.html @@ -5,7 +5,7 @@ makes xcms_id format liked ROI unique id - + @@ -68,8 +68,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/annotationStream.compounds.html b/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/annotationStream.compounds.html index 4b34868963..a3bf56b7ad 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/annotationStream.compounds.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/annotationStream.compounds.html @@ -5,7 +5,7 @@ Construct a basic metabolite annotation data collection - + @@ -79,8 +79,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/annotationStream.html b/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/annotationStream.html index 75fb94fc9b..5f96d9e8a8 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/annotationStream.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/annotationStream.html @@ -5,7 +5,7 @@ Construct a basic metabolite annotation data collection - + @@ -79,8 +79,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/cbind.metainfo.html b/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/cbind.metainfo.html index 7ba24d5da3..d1ba1a7a3f 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/cbind.metainfo.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/cbind.metainfo.html @@ -5,7 +5,7 @@ cbind.metainfo - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/excludeFeatures.html b/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/excludeFeatures.html index 03352bc9e0..3475883134 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/excludeFeatures.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/excludeFeatures.html @@ -5,7 +5,7 @@ removes all of the annotation result which is not - + @@ -91,8 +91,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/getMetadata.html b/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/getMetadata.html index 0ad3bf6b2c..eb2f191a64 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/getMetadata.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/getMetadata.html @@ -5,7 +5,7 @@ get metabolite annotation metadata by a set of given unique reference id - + @@ -71,8 +71,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/has.metal_ion.html b/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/has.metal_ion.html index deaa190613..858d16bef4 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/has.metal_ion.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/has.metal_ion.html @@ -5,7 +5,7 @@ Check the formula string has metal ion inside? - + @@ -67,8 +67,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/load_asQueryHits.html b/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/load_asQueryHits.html index 8109799049..12f473b511 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/load_asQueryHits.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/load_asQueryHits.html @@ -5,7 +5,7 @@ load_asQueryHits - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/mass_search.index.html b/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/mass_search.index.html index d05d276d48..8c036dc42b 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/mass_search.index.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/mass_search.index.html @@ -5,7 +5,7 @@ - + @@ -76,8 +76,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/ms1_handler.html b/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/ms1_handler.html index 5330bdd568..3dba9661bc 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/ms1_handler.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/ms1_handler.html @@ -5,7 +5,7 @@ a generic function for handle ms1 search - + @@ -76,8 +76,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/ms1_search.html b/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/ms1_search.html index d7199326d5..c99054165c 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/ms1_search.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/ms1_search.html @@ -5,7 +5,7 @@ get duplictaed raw annotation results. - + @@ -76,8 +76,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/parseLipidName.html b/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/parseLipidName.html index 44a5df3625..264508c175 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/parseLipidName.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/parseLipidName.html @@ -5,7 +5,7 @@ Parse the lipid names - + @@ -72,8 +72,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/precursorIon.html b/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/precursorIon.html index 58469a109a..bc366c456c 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/precursorIon.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/precursorIon.html @@ -5,7 +5,7 @@ parse the precursor type calculator - + @@ -63,8 +63,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/queryByMass.html b/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/queryByMass.html index c3e89391e1..1347e30b20 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/queryByMass.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/queryByMass.html @@ -5,7 +5,7 @@ queryByMass - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/searchMz.html b/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/searchMz.html index 203414ce6c..227c84d60f 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/searchMz.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/searchMz.html @@ -5,7 +5,7 @@ Found the best matched mz value with the target **`exactMass`** - + @@ -78,8 +78,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/uniqueFeatures.html b/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/uniqueFeatures.html index 310ed389e8..6c0fdcfea2 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/uniqueFeatures.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/uniqueFeatures.html @@ -5,7 +5,7 @@ unique of the peak annotation features - + @@ -86,8 +86,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/verify_cas_number.html b/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/verify_cas_number.html index 168210c437..1365cd932a 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/verify_cas_number.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/metadb/verify_cas_number.html @@ -5,7 +5,7 @@ verify that the given cas registry number is correct or not - + @@ -67,8 +67,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/mzPack/convertTo_mzXML.html b/Rscript/Library/mzkit_app/vignettes/mzkit/mzPack/convertTo_mzXML.html index f697dfdb65..289c97c185 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/mzPack/convertTo_mzXML.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/mzPack/convertTo_mzXML.html @@ -5,7 +5,7 @@ method for write mzpack data object as a mzML file - + @@ -71,8 +71,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/mzPack/getSampleTags.html b/Rscript/Library/mzkit_app/vignettes/mzkit/mzPack/getSampleTags.html index b301403567..6a2b3e4efa 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/mzPack/getSampleTags.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/mzPack/getSampleTags.html @@ -5,7 +5,7 @@ get all of the sample file data tags from target mzpack file - + @@ -66,8 +66,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/mzPack/ls.html b/Rscript/Library/mzkit_app/vignettes/mzkit/mzPack/ls.html index bb2c427493..9bc418b314 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/mzPack/ls.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/mzPack/ls.html @@ -5,7 +5,7 @@ Get object list inside the MS packdata - + @@ -72,8 +72,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/mzPack/metadata.html b/Rscript/Library/mzkit_app/vignettes/mzkit/mzPack/metadata.html index 003ccdc7aa..0fd1efdb55 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/mzPack/metadata.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/mzPack/metadata.html @@ -5,7 +5,7 @@ get metadata list from a specific ms1 scan - + @@ -74,8 +74,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/mzPack/mzpack.html b/Rscript/Library/mzkit_app/vignettes/mzkit/mzPack/mzpack.html index 1c47b9e08b..e552bba53a 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/mzPack/mzpack.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/mzPack/mzpack.html @@ -5,7 +5,7 @@ open a mzpack data object reader, not read all data into memory in one time. - + @@ -69,8 +69,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/mzPack/mzwork.html b/Rscript/Library/mzkit_app/vignettes/mzkit/mzPack/mzwork.html index 0bb34daf56..fb6264ac8a 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/mzPack/mzwork.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/mzPack/mzwork.html @@ -5,7 +5,7 @@ open a mzwork package file - + @@ -67,8 +67,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/mzPack/open.mzwork.html b/Rscript/Library/mzkit_app/vignettes/mzkit/mzPack/open.mzwork.html index a79ba4ad08..8ac5e0269d 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/mzPack/open.mzwork.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/mzPack/open.mzwork.html @@ -5,7 +5,7 @@ open mzwork file and then populate all of the mzpack raw data file - + @@ -63,8 +63,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/mzPack/packData.html b/Rscript/Library/mzkit_app/vignettes/mzkit/mzPack/packData.html index b4cc120049..0c8a7fe064 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/mzPack/packData.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/mzPack/packData.html @@ -5,7 +5,7 @@ pack mzkit ms2 peaks data as a mzpack data object - + @@ -75,8 +75,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/mzPack/packStream.html b/Rscript/Library/mzkit_app/vignettes/mzkit/mzPack/packStream.html index 7cac64c677..a0224df672 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/mzPack/packStream.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/mzPack/packStream.html @@ -5,7 +5,7 @@ write mzPack in v2 format - + @@ -71,8 +71,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/mzPack/pack_ms1.html b/Rscript/Library/mzkit_app/vignettes/mzkit/mzPack/pack_ms1.html index 941bf1f439..0cd3973d4c 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/mzPack/pack_ms1.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/mzPack/pack_ms1.html @@ -5,7 +5,7 @@ pack a given ms2 spectrum collection as a single ms1 scan product - + @@ -72,8 +72,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/mzPack/readFileCache.html b/Rscript/Library/mzkit_app/vignettes/mzkit/mzPack/readFileCache.html index e7c5dd2679..6c753dd108 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/mzPack/readFileCache.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/mzPack/readFileCache.html @@ -5,7 +5,7 @@ get mzpack object from mzwork archive - + @@ -72,8 +72,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/mzPack/removeSciexNoise.html b/Rscript/Library/mzkit_app/vignettes/mzkit/mzPack/removeSciexNoise.html index 14f9187d94..19d4957157 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/mzPack/removeSciexNoise.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/mzPack/removeSciexNoise.html @@ -5,7 +5,7 @@ Removes the sciex AB5600 noise data from the MS2 raw data - + @@ -68,8 +68,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/mzPack/scaninfo.html b/Rscript/Library/mzkit_app/vignettes/mzkit/mzPack/scaninfo.html index 39bc6aa202..db77e8e17c 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/mzPack/scaninfo.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/mzPack/scaninfo.html @@ -5,7 +5,7 @@ get ms scan information metadata list - + @@ -74,8 +74,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/mzPack/split_samples.html b/Rscript/Library/mzkit_app/vignettes/mzkit/mzPack/split_samples.html index f1618e276c..ab12bf656b 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/mzPack/split_samples.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/mzPack/split_samples.html @@ -5,7 +5,7 @@ try to split target mzpack file into multiple parts based on the sample tags - + @@ -63,8 +63,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/BPC.html b/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/BPC.html index c0b695283c..958ab77a71 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/BPC.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/BPC.html @@ -5,7 +5,7 @@ Get BPC from the mzpack layer reader - + @@ -67,8 +67,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/TIC.html b/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/TIC.html index b17adfe408..ec732902d5 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/TIC.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/TIC.html @@ -5,7 +5,7 @@ Get TIC from the mzpack layer reader - + @@ -66,8 +66,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/as.mzpack.html b/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/as.mzpack.html index 0e23265fcf..544aba7e96 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/as.mzpack.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/as.mzpack.html @@ -5,7 +5,7 @@ convert assembly file to mzpack format data object - + @@ -77,8 +77,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/load.chromatogram.html b/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/load.chromatogram.html index f3e21fd07e..ebfb869214 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/load.chromatogram.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/load.chromatogram.html @@ -5,7 +5,7 @@ load chromatogram data from the raw file data - + @@ -68,8 +68,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/load.stream.html b/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/load.stream.html index 72158fc907..6183513a6d 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/load.stream.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/load.stream.html @@ -5,7 +5,7 @@ load the unify mzweb scan stream data from the mzml/mzxml raw scan data stream. - + @@ -72,8 +72,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/loadXcmsRData.html b/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/loadXcmsRData.html index c4cffa0e67..272da11d2d 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/loadXcmsRData.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/loadXcmsRData.html @@ -5,7 +5,7 @@ load the xcms cache dataset - + @@ -67,8 +67,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/mass_calibration.html b/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/mass_calibration.html index 100ef58d0d..444483c4dd 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/mass_calibration.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/mass_calibration.html @@ -5,7 +5,7 @@ do mass calibration - + @@ -72,8 +72,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/ms1_peaks.html b/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/ms1_peaks.html index 1a92d7ad42..3dc2f03572 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/ms1_peaks.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/ms1_peaks.html @@ -5,7 +5,7 @@ get a overview ms1 spectrum data from the mzpack raw data - + @@ -87,8 +87,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/ms1_scans.html b/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/ms1_scans.html index 28dba1bfe9..acc9f2ca8c 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/ms1_scans.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/ms1_scans.html @@ -5,7 +5,7 @@ get all ms1 scan data points - + @@ -76,8 +76,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/ms2_peaks.html b/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/ms2_peaks.html index ce14d74adb..1fa45ebc46 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/ms2_peaks.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/ms2_peaks.html @@ -5,7 +5,7 @@ extract ms2 peaks data from the mzpack data object - + @@ -104,8 +104,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/open.html b/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/open.html index 5c74463d83..acb183f01c 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/open.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/open.html @@ -5,7 +5,7 @@ open a mzpack data file lazy reader - + @@ -63,8 +63,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/open.mzpack.html b/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/open.mzpack.html index 0d7aca0566..26f68e76a2 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/open.mzpack.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/open.mzpack.html @@ -5,7 +5,7 @@ open a raw data files in common raw data format and then returns - + @@ -64,8 +64,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/open_mzpack.xml.html b/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/open_mzpack.xml.html index 8fcfbf3b58..747d4ea27b 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/open_mzpack.xml.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/open_mzpack.xml.html @@ -5,7 +5,7 @@ open mzpack data from a raw data file in xml file format. - + @@ -72,8 +72,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/packBin.html b/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/packBin.html index 8de629172c..22535c8e36 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/packBin.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/packBin.html @@ -5,7 +5,7 @@ write binary format of mzweb stream data - + @@ -67,8 +67,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/parse.scanMs.html b/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/parse.scanMs.html index 493629db50..eb13f84f52 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/parse.scanMs.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/parse.scanMs.html @@ -5,7 +5,7 @@ Parse the ms scan data from a given raw byte stream data - + @@ -72,8 +72,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/parse_base64.html b/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/parse_base64.html index b1bce97b78..0677820164 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/parse_base64.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/parse_base64.html @@ -5,7 +5,7 @@ Parse the given network base64 data as spectrum - + @@ -82,8 +82,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/read.cache.html b/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/read.cache.html index 2e220e7c29..4adbbacc4c 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/read.cache.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/read.cache.html @@ -5,7 +5,7 @@ read the mzPack data file liked simple msn cached data - + @@ -63,8 +63,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/setThumbnail.html b/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/setThumbnail.html index b93390a3a8..bd4d983d87 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/setThumbnail.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/setThumbnail.html @@ -5,7 +5,7 @@ set thumbnail image to the raw data file - + @@ -73,8 +73,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/write.cache.html b/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/write.cache.html index b56a986ebf..a3b80d1270 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/write.cache.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/write.cache.html @@ -5,7 +5,7 @@ write binary format of mzweb stream data - + @@ -68,8 +68,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/write.cdf.html b/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/write.cdf.html index b823b73b0e..1ce66ada00 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/write.cdf.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/write.cdf.html @@ -5,7 +5,7 @@ write.cdf - + @@ -61,8 +61,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/write.mzPack.html b/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/write.mzPack.html index 66b932b801..1a6602aa77 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/write.mzPack.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/write.mzPack.html @@ -5,7 +5,7 @@ write version 2 format of the mzpack by default - + @@ -77,8 +77,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/write.text_cache.html b/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/write.text_cache.html index d7feefe0a4..7ba3f4df42 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/write.text_cache.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/mzweb/write.text_cache.html @@ -5,7 +5,7 @@ write ASCII text format of mzweb stream - + @@ -76,8 +76,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/CID.html b/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/CID.html index a75bd7bdb9..06817eeec2 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/CID.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/CID.html @@ -5,7 +5,7 @@ query cid from pubchem database - + @@ -78,8 +78,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/SID_map.html b/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/SID_map.html index b567757c33..e1dd1a1500 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/SID_map.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/SID_map.html @@ -5,7 +5,7 @@ parse the pubchem sid map data file - + @@ -75,8 +75,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/image_fly.html b/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/image_fly.html index 93ace336d7..e18fd9e36e 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/image_fly.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/image_fly.html @@ -5,7 +5,7 @@ Request the metabolite structure image via the pubchem image_fly api - + @@ -78,8 +78,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/mesh_background.html b/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/mesh_background.html index b972bad8eb..61049e5ace 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/mesh_background.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/mesh_background.html @@ -5,7 +5,7 @@ create MeSH ontology gsea background based on the mesh tree - + @@ -68,8 +68,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/mesh_level1.html b/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/mesh_level1.html index ec2f28a011..eb36ab09d5 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/mesh_level1.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/mesh_level1.html @@ -5,7 +5,7 @@ gets the level1 term label of the mesh tree - + @@ -63,8 +63,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/metadata.pugView.html b/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/metadata.pugView.html index aa2e9694d5..fa37b62a96 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/metadata.pugView.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/metadata.pugView.html @@ -5,7 +5,7 @@ extract the compound annotation data - + @@ -63,8 +63,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/pubchem_url.html b/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/pubchem_url.html index 1057108a07..ae1f9c9be7 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/pubchem_url.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/pubchem_url.html @@ -5,7 +5,7 @@ Generate the url for get pubchem pugviews data object - + @@ -63,8 +63,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/pugView.html b/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/pugView.html index b1ed4cbf7e..f60860ac3b 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/pugView.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/pugView.html @@ -5,7 +5,7 @@ query pubchem data via a given cid value - + @@ -85,8 +85,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/query.external.html b/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/query.external.html index 8fe6ca24ac..aea4cb6c3c 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/query.external.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/query.external.html @@ -5,7 +5,7 @@ query of the pathways, taxonomy and reaction - + @@ -73,8 +73,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/query.html b/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/query.html index f9632d3ab6..23cf8cb9f0 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/query.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/query.html @@ -5,7 +5,7 @@ query of the pubchem database - + @@ -68,8 +68,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/query.knowlegde_graph.html b/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/query.knowlegde_graph.html index ee7464ab63..57f5d5e715 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/query.knowlegde_graph.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/query.knowlegde_graph.html @@ -5,7 +5,7 @@ Query the compound related biological context information from pubchem - + @@ -75,8 +75,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/read.mesh_tree.html b/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/read.mesh_tree.html index b1b3c08d77..4403873dac 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/read.mesh_tree.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/read.mesh_tree.html @@ -5,7 +5,7 @@ Parse the mesh ontology tree - + @@ -67,8 +67,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/read.pubmed.html b/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/read.pubmed.html index f3fff107b8..a83244f46a 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/read.pubmed.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/read.pubmed.html @@ -5,7 +5,7 @@ read pubmed data table files - + @@ -73,8 +73,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/read.pugView.html b/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/read.pugView.html index 0537481860..a406cbff55 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/read.pugView.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/read.pugView.html @@ -5,7 +5,7 @@ read xml text and then parse as pugview record data object - + @@ -63,8 +63,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/read.webquery.html b/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/read.webquery.html index 99f842f4d6..c14df9d533 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/read.webquery.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/read.webquery.html @@ -5,7 +5,7 @@ read the pubchem webquery summary xml file - + @@ -73,8 +73,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/resolve_repository.html b/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/resolve_repository.html index f7a40d900e..fb7aa0272f 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/resolve_repository.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/pubchem_kit/resolve_repository.html @@ -5,7 +5,7 @@ load pubchem repository - + @@ -63,8 +63,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/spectrumTree/addBucket.html b/Rscript/Library/mzkit_app/vignettes/mzkit/spectrumTree/addBucket.html index d59e2b8827..1fc17c811e 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/spectrumTree/addBucket.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/spectrumTree/addBucket.html @@ -5,7 +5,7 @@ push the reference spectrum data into the spectrum reference tree library - + @@ -84,8 +84,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/spectrumTree/compress.html b/Rscript/Library/mzkit_app/vignettes/mzkit/spectrumTree/compress.html index 44d9b5e390..c88f3677e0 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/spectrumTree/compress.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/spectrumTree/compress.html @@ -5,7 +5,7 @@ Compress and make cleanup of the spectrum library - + @@ -78,8 +78,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/spectrumTree/dotcutoff.html b/Rscript/Library/mzkit_app/vignettes/mzkit/spectrumTree/dotcutoff.html index 67a9b67f96..4dc19c8cca 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/spectrumTree/dotcutoff.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/spectrumTree/dotcutoff.html @@ -5,7 +5,7 @@ set dot cutoff parameter for the cos score similarity algorithm - + @@ -67,8 +67,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/spectrumTree/embedding.html b/Rscript/Library/mzkit_app/vignettes/mzkit/spectrumTree/embedding.html index 4dcc548760..d43333f19e 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/spectrumTree/embedding.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/spectrumTree/embedding.html @@ -5,7 +5,7 @@ do embedding of the spectrum data - + @@ -72,8 +72,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/spectrumTree/export_spectrum.html b/Rscript/Library/mzkit_app/vignettes/mzkit/spectrumTree/export_spectrum.html index a74c5c99db..be180e4411 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/spectrumTree/export_spectrum.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/spectrumTree/export_spectrum.html @@ -5,7 +5,7 @@ export all reference spectrum from the given library object - + @@ -63,8 +63,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/spectrumTree/get_testSample.html b/Rscript/Library/mzkit_app/vignettes/mzkit/spectrumTree/get_testSample.html index 423036d3f3..7911e58212 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/spectrumTree/get_testSample.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/spectrumTree/get_testSample.html @@ -5,7 +5,7 @@ Extract the test sample data for run evaluation of the annotation workflow - + @@ -74,8 +74,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/spectrumTree/jaccardSet.html b/Rscript/Library/mzkit_app/vignettes/mzkit/spectrumTree/jaccardSet.html index 2bdfd86630..4d583c3f04 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/spectrumTree/jaccardSet.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/spectrumTree/jaccardSet.html @@ -5,7 +5,7 @@ construct a fragment set library for run spectrum search in jaccard index matches method - + @@ -86,8 +86,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/spectrumTree/new.html b/Rscript/Library/mzkit_app/vignettes/mzkit/spectrumTree/new.html index 6ca6b7ca4e..6bf0ef2cc8 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/spectrumTree/new.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/spectrumTree/new.html @@ -5,7 +5,7 @@ create new reference spectrum database - + @@ -68,8 +68,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/spectrumTree/open.html b/Rscript/Library/mzkit_app/vignettes/mzkit/spectrumTree/open.html index f48896f1b5..fc31914193 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/spectrumTree/open.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/spectrumTree/open.html @@ -5,7 +5,7 @@ open the spectrum reference database - + @@ -84,8 +84,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/spectrumTree/parallel.html b/Rscript/Library/mzkit_app/vignettes/mzkit/spectrumTree/parallel.html index a44b550a02..c685ee04d8 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/spectrumTree/parallel.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/spectrumTree/parallel.html @@ -5,7 +5,7 @@ enable internal parallel for the spectrum alignment search? - + @@ -67,8 +67,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/spectrumTree/query.html b/Rscript/Library/mzkit_app/vignettes/mzkit/spectrumTree/query.html index 825f7c3fa9..44949bf884 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/spectrumTree/query.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/spectrumTree/query.html @@ -5,7 +5,7 @@ do spectrum family alignment via cos similarity - + @@ -88,8 +88,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/spectrumTree/readpack.html b/Rscript/Library/mzkit_app/vignettes/mzkit/spectrumTree/readpack.html index 0650b8b7f8..63a06b3410 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/spectrumTree/readpack.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/spectrumTree/readpack.html @@ -5,7 +5,7 @@ open the spectrum pack reference database file - + @@ -67,8 +67,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/z_assembler/z_assembler.html b/Rscript/Library/mzkit_app/vignettes/mzkit/z_assembler/z_assembler.html index 1481d0d214..4ec2edc2e8 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/z_assembler/z_assembler.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/z_assembler/z_assembler.html @@ -5,7 +5,7 @@ Create mzpack object for ms-imaging in 3D - + @@ -63,8 +63,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/z_assembler/z_header.html b/Rscript/Library/mzkit_app/vignettes/mzkit/z_assembler/z_header.html index 463a663ccf..be599729f1 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/z_assembler/z_header.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/z_assembler/z_header.html @@ -5,7 +5,7 @@ create the volume file header data - + @@ -68,8 +68,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzkit/z_assembler/z_volume.html b/Rscript/Library/mzkit_app/vignettes/mzkit/z_assembler/z_volume.html index a98d9d429d..8655d07c14 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzkit/z_assembler/z_volume.html +++ b/Rscript/Library/mzkit_app/vignettes/mzkit/z_assembler/z_volume.html @@ -5,7 +5,7 @@ create a simple 3d volume model for mzkit workbench - + @@ -73,8 +73,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzplot/ChemicalDraw/KCFDraw.html b/Rscript/Library/mzkit_app/vignettes/mzplot/ChemicalDraw/KCFDraw.html index 5afbb0833c..dcb6b4d703 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzplot/ChemicalDraw/KCFDraw.html +++ b/Rscript/Library/mzkit_app/vignettes/mzplot/ChemicalDraw/KCFDraw.html @@ -5,7 +5,7 @@ KCFDraw - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzplot/ChemicalDraw/as.kcf.html b/Rscript/Library/mzkit_app/vignettes/mzplot/ChemicalDraw/as.kcf.html index 5bd724a916..ffc2d1e051 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzplot/ChemicalDraw/as.kcf.html +++ b/Rscript/Library/mzkit_app/vignettes/mzplot/ChemicalDraw/as.kcf.html @@ -5,7 +5,7 @@ as.kcf - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/FilterMz.html b/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/FilterMz.html index 8cabf2de0b..bad5daca02 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/FilterMz.html +++ b/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/FilterMz.html @@ -5,7 +5,7 @@ Extract a spectrum matrix object from MSI data by a given set of m/z values - + @@ -81,8 +81,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/MS1.html b/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/MS1.html index 9dd540c07b..9e2678550d 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/MS1.html +++ b/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/MS1.html @@ -5,7 +5,7 @@ get the ms1 spectrum data in a specific pixel position - + @@ -92,8 +92,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/MSI_coverage.html b/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/MSI_coverage.html index 42df176d23..1e7ec3f9db 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/MSI_coverage.html +++ b/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/MSI_coverage.html @@ -5,7 +5,7 @@ - + @@ -72,8 +72,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/MSI_summary.scaleMax.html b/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/MSI_summary.scaleMax.html index 508f331e45..8ba0b6270e 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/MSI_summary.scaleMax.html +++ b/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/MSI_summary.scaleMax.html @@ -5,7 +5,7 @@ Get the max intensity value via TrIQ or quantile cutoff - + @@ -81,8 +81,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/MSIlayer.html b/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/MSIlayer.html index 19b6ffe35d..e39efccb62 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/MSIlayer.html +++ b/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/MSIlayer.html @@ -5,7 +5,7 @@ get MSI pixels layer via given ``m/z`` value. - + @@ -89,8 +89,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/MeasureMSIions.html b/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/MeasureMSIions.html index 17af30637d..6514a353df 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/MeasureMSIions.html +++ b/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/MeasureMSIions.html @@ -5,7 +5,7 @@ - + @@ -95,8 +95,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/TrIQ.html b/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/TrIQ.html index f8da29ea4f..20f724ef81 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/TrIQ.html +++ b/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/TrIQ.html @@ -5,7 +5,7 @@ Contrast optimization of mass spectrometry imaging(MSI) data - + @@ -73,8 +73,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/apply_raster_filter.html b/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/apply_raster_filter.html index 7d3569cc06..f2c9d4f389 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/apply_raster_filter.html +++ b/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/apply_raster_filter.html @@ -5,7 +5,7 @@ apply a single filter or a filter pipeline - + @@ -67,8 +67,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/as.pixels.html b/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/as.pixels.html index 7ff862f9f5..4fa6189f18 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/as.pixels.html +++ b/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/as.pixels.html @@ -5,7 +5,7 @@ extract the pixel [x,y] information for all of - + @@ -69,8 +69,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/assert.html b/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/assert.html index 47e086e3b1..48f5aeb73b 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/assert.html +++ b/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/assert.html @@ -5,7 +5,7 @@ test of a given MSI layer is target? - + @@ -69,8 +69,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/defaultFilter.html b/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/defaultFilter.html index 9d98c9f86e..259c4198dc 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/defaultFilter.html +++ b/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/defaultFilter.html @@ -5,7 +5,7 @@ get the default ms-imaging filter pipeline - + @@ -65,8 +65,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/intensity.html b/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/intensity.html index 6f31f927cd..7b08d50f8c 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/intensity.html +++ b/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/intensity.html @@ -5,7 +5,7 @@ Get intensity data vector from a given MS-imaging layer - + @@ -72,8 +72,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/intensityFilter.html b/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/intensityFilter.html index cf45e6e4b7..33d3a9f2ae 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/intensityFilter.html +++ b/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/intensityFilter.html @@ -5,7 +5,7 @@ intensityFilter - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/intensityLimits.html b/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/intensityLimits.html index a653dbae58..1e0b7d66bf 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/intensityLimits.html +++ b/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/intensityLimits.html @@ -5,7 +5,7 @@ trim the intensity data value in a pixels of a ion MS-Imaging layer - + @@ -72,8 +72,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/ionLayers.html b/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/ionLayers.html index e970f669d3..095599ce37 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/ionLayers.html +++ b/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/ionLayers.html @@ -5,7 +5,7 @@ load the raw pixels data from imzML file - + @@ -78,8 +78,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/knnFill.html b/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/knnFill.html index 28921402dc..23830209d3 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/knnFill.html +++ b/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/knnFill.html @@ -5,7 +5,7 @@ do pixel interpolation for run MS-imaging - + @@ -77,8 +77,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/layer.html b/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/layer.html index 6f41235523..c50d5395a8 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/layer.html +++ b/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/layer.html @@ -5,7 +5,7 @@ render a ms-imaging layer by a specific ``m/z`` scan. - + @@ -90,8 +90,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/parseFilters.html b/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/parseFilters.html index 28d738a2b1..670745afcc 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/parseFilters.html +++ b/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/parseFilters.html @@ -5,7 +5,7 @@ - + @@ -63,8 +63,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/pixel.html b/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/pixel.html index add79a6973..ef3ed67559 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/pixel.html +++ b/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/pixel.html @@ -5,7 +5,7 @@ get the spatial spot pixel data - + @@ -71,8 +71,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/read.mzImage.html b/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/read.mzImage.html index 053bac77b4..92e56a2676 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/read.mzImage.html +++ b/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/read.mzImage.html @@ -5,7 +5,7 @@ open the existed mzImage cache file - + @@ -67,8 +67,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/render.html b/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/render.html index 3240720c9c..a5914f7cdf 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/render.html +++ b/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/render.html @@ -5,7 +5,7 @@ MS-imaging of the MSI summary data result. - + @@ -111,8 +111,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/rgb.html b/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/rgb.html index 076d6e0095..a39f8ee3e3 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/rgb.html +++ b/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/rgb.html @@ -5,7 +5,7 @@ rendering ions MSI in (R,G,B) color channels - + @@ -88,8 +88,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/split.layer.html b/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/split.layer.html index a61a0d442b..71e656a1ea 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/split.layer.html +++ b/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/split.layer.html @@ -5,7 +5,7 @@ split the ms-imaging layer into multiple parts - + @@ -71,8 +71,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/sum_layers.html b/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/sum_layers.html index 311c17e213..bc447b0643 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/sum_layers.html +++ b/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/sum_layers.html @@ -5,7 +5,7 @@ merge multiple layers via intensity sum - + @@ -69,8 +69,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/tag_layers.html b/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/tag_layers.html index 53d3535780..bf6061a1f4 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/tag_layers.html +++ b/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/tag_layers.html @@ -5,7 +5,7 @@ set cluster tags to the pixel tag property data - + @@ -72,8 +72,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/viewer.html b/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/viewer.html index 06e847551a..5fcb08acd4 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/viewer.html +++ b/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/viewer.html @@ -5,7 +5,7 @@ load imzML data into the ms-imaging render - + @@ -63,8 +63,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/write.mzImage.html b/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/write.mzImage.html index c7da5dccc8..a85f05d0f7 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/write.mzImage.html +++ b/Rscript/Library/mzkit_app/vignettes/mzplot/MsImaging/write.mzImage.html @@ -5,7 +5,7 @@ write mzImage data file - + @@ -73,8 +73,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzplot/NMR/plot_nmr.html b/Rscript/Library/mzkit_app/vignettes/mzplot/NMR/plot_nmr.html index 0e101c9ae6..fea394f22e 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzplot/NMR/plot_nmr.html +++ b/Rscript/Library/mzkit_app/vignettes/mzplot/NMR/plot_nmr.html @@ -5,7 +5,7 @@ plot_nmr - + @@ -62,8 +62,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzplot/tissue/RSD.html b/Rscript/Library/mzkit_app/vignettes/mzplot/tissue/RSD.html index bd8396575e..99108d9fe1 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzplot/tissue/RSD.html +++ b/Rscript/Library/mzkit_app/vignettes/mzplot/tissue/RSD.html @@ -5,7 +5,7 @@ evaluate the spatial RSD of a specific channel - + @@ -73,8 +73,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzplot/tissue/heatmap_layer.html b/Rscript/Library/mzkit_app/vignettes/mzplot/tissue/heatmap_layer.html index 211e97bb51..dcbfeec69f 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzplot/tissue/heatmap_layer.html +++ b/Rscript/Library/mzkit_app/vignettes/mzplot/tissue/heatmap_layer.html @@ -5,7 +5,7 @@ generates heatmap value - + @@ -74,8 +74,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzplot/tissue/mark_nucleus.html b/Rscript/Library/mzkit_app/vignettes/mzplot/tissue/mark_nucleus.html index 44198388f3..e12f832aef 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzplot/tissue/mark_nucleus.html +++ b/Rscript/Library/mzkit_app/vignettes/mzplot/tissue/mark_nucleus.html @@ -5,7 +5,7 @@ extract the possible nucleus pixel points from the image - + @@ -76,8 +76,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzplot/tissue/scan_tissue.html b/Rscript/Library/mzkit_app/vignettes/mzplot/tissue/scan_tissue.html index 6b1df3462a..64e24d6503 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzplot/tissue/scan_tissue.html +++ b/Rscript/Library/mzkit_app/vignettes/mzplot/tissue/scan_tissue.html @@ -5,7 +5,7 @@ analysis the HE-stain image by blocks - + @@ -83,8 +83,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzplot/visual/gcxgc_heatmap.html b/Rscript/Library/mzkit_app/vignettes/mzplot/visual/gcxgc_heatmap.html index 09b9eb6c29..56c55445f2 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzplot/visual/gcxgc_heatmap.html +++ b/Rscript/Library/mzkit_app/vignettes/mzplot/visual/gcxgc_heatmap.html @@ -5,7 +5,7 @@ - + @@ -78,8 +78,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzplot/visual/mass_spectrum.plot.html b/Rscript/Library/mzkit_app/vignettes/mzplot/visual/mass_spectrum.plot.html index 24c4e9fb19..f5738cf86a 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzplot/visual/mass_spectrum.plot.html +++ b/Rscript/Library/mzkit_app/vignettes/mzplot/visual/mass_spectrum.plot.html @@ -5,7 +5,7 @@ Plot of the mass spectrum - + @@ -99,8 +99,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzplot/visual/parse.spectrum_alignment.html b/Rscript/Library/mzkit_app/vignettes/mzplot/visual/parse.spectrum_alignment.html index 579b075bb4..cc2c8cacac 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzplot/visual/parse.spectrum_alignment.html +++ b/Rscript/Library/mzkit_app/vignettes/mzplot/visual/parse.spectrum_alignment.html @@ -5,7 +5,7 @@ parse.spectrum_alignment - + @@ -60,8 +60,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzplot/visual/plot.UV_signals.html b/Rscript/Library/mzkit_app/vignettes/mzplot/visual/plot.UV_signals.html index 2690690a43..73ec083d88 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzplot/visual/plot.UV_signals.html +++ b/Rscript/Library/mzkit_app/vignettes/mzplot/visual/plot.UV_signals.html @@ -5,7 +5,7 @@ visual of the UV spectrum - + @@ -97,8 +97,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzplot/visual/plotNetworkClusterHistogram.html b/Rscript/Library/mzkit_app/vignettes/mzplot/visual/plotNetworkClusterHistogram.html index d7709d217e..951831234d 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzplot/visual/plotNetworkClusterHistogram.html +++ b/Rscript/Library/mzkit_app/vignettes/mzplot/visual/plotNetworkClusterHistogram.html @@ -5,7 +5,7 @@ Plot cluster size histogram on RT dimension - + @@ -82,8 +82,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzplot/visual/raw_scatter.html b/Rscript/Library/mzkit_app/vignettes/mzplot/visual/raw_scatter.html index 9365b40f7d..1a30db187e 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzplot/visual/raw_scatter.html +++ b/Rscript/Library/mzkit_app/vignettes/mzplot/visual/raw_scatter.html @@ -5,7 +5,7 @@ plot raw scatter matrix based on a given sequence of ms1 scans data - + @@ -71,8 +71,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzplot/visual/raw_snapshot3D.html b/Rscript/Library/mzkit_app/vignettes/mzplot/visual/raw_snapshot3D.html index 3ef34b1925..6b10bbfa27 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzplot/visual/raw_snapshot3D.html +++ b/Rscript/Library/mzkit_app/vignettes/mzplot/visual/raw_snapshot3D.html @@ -5,7 +5,7 @@ plot raw XIC matrix based on a given sequence of ms1 scans data - + @@ -77,8 +77,8 @@

Examples

- - + + \ No newline at end of file diff --git a/Rscript/Library/mzkit_app/vignettes/mzplot/visual/xic_scatter_density.html b/Rscript/Library/mzkit_app/vignettes/mzplot/visual/xic_scatter_density.html index 3c97228194..d8daf2d975 100644 --- a/Rscript/Library/mzkit_app/vignettes/mzplot/visual/xic_scatter_density.html +++ b/Rscript/Library/mzkit_app/vignettes/mzplot/visual/xic_scatter_density.html @@ -5,7 +5,7 @@ make visualization of the XIC scatters - + @@ -67,8 +67,8 @@

Examples

- - + + \ No newline at end of file diff --git a/src/assembly/Comprehensive/Comprehensive.NET5.vbproj b/src/assembly/Comprehensive/Comprehensive.NET5.vbproj index 152abe3d81..9485f6bd9d 100644 --- a/src/assembly/Comprehensive/Comprehensive.NET5.vbproj +++ b/src/assembly/Comprehensive/Comprehensive.NET5.vbproj @@ -16,6 +16,8 @@ true true + True + Comprehensive Mass Spectrum Tools @@ -151,6 +153,7 @@ + diff --git a/src/assembly/Comprehensive/GCxGC/D2Chromatogram.vb b/src/assembly/Comprehensive/GCxGC/D2Chromatogram.vb index b372dd48e4..f931bf73b8 100644 --- a/src/assembly/Comprehensive/GCxGC/D2Chromatogram.vb +++ b/src/assembly/Comprehensive/GCxGC/D2Chromatogram.vb @@ -58,12 +58,10 @@ #End Region Imports System.IO -Imports System.Runtime.CompilerServices Imports BioNovoGene.Analytical.MassSpectrometry.Assembly.mzData.mzWebCache +Imports BioNovoGene.Analytical.MassSpectrometry.GCxGC Imports BioNovoGene.Analytical.MassSpectrometry.Math.Chromatogram Imports Microsoft.VisualBasic.ComponentModel.Collection -Imports Microsoft.VisualBasic.ComponentModel.Collection.Generic -Imports Microsoft.VisualBasic.ComponentModel.Ranges.Model Imports Microsoft.VisualBasic.DataStorage.netCDF Imports Microsoft.VisualBasic.DataStorage.netCDF.Components Imports Microsoft.VisualBasic.DataStorage.netCDF.Data @@ -77,54 +75,7 @@ Imports Microsoft.VisualBasic.Linq ''' ''' is a collection of the data. ''' -Public Class D2Chromatogram : Implements IReadOnlyId, INamedValue - - Public Property scan_time As Double - Public Property intensity As Double - Public Property scan_id As String Implements INamedValue.Key, IReadOnlyId.Identity - - ''' - ''' chromatogram data 2d - ''' - ''' - Public Property chromatogram As ChromatogramTick() - - Default Public ReadOnly Property getTick(i As DoubleRange) As ChromatogramTick() - Get - Return chromatogram.Where(Function(a) i.IsInside(a.Time)).ToArray - End Get - End Property - - Default Public ReadOnly Property getTick(i As Integer) As ChromatogramTick - - Get - Return _chromatogram(i) - End Get - End Property - - Public ReadOnly Property size As Integer - - Get - Return chromatogram.Length - End Get - End Property - - Sub New() - End Sub - - Sub New(t1 As Double) - scan_time = t1 - End Sub - - Sub New(t1 As Double, id As String) - scan_id = id - scan_time = t1 - End Sub - - - Public Overrides Function ToString() As String - Return $"{intensity.ToString("G3")}@{scan_time.ToString("F2")}" - End Function +Public Module D2Chromatogram ''' ''' Export GCxGC data in mzkit cdf format @@ -132,7 +83,7 @@ Public Class D2Chromatogram : Implements IReadOnlyId, INamedValue ''' ''' ''' - Public Shared Function EncodeCDF(gcxgc As IEnumerable(Of D2Chromatogram), file As Stream) As Boolean + Public Function EncodeCDF(gcxgc As IEnumerable(Of Chromatogram2DScan), file As Stream) As Boolean Using writer As New CDFWriter(file) Dim i As i32 = 1 Dim size As New Dictionary(Of String, Dimension) @@ -140,7 +91,7 @@ Public Class D2Chromatogram : Implements IReadOnlyId, INamedValue Dim dims As Dimension Dim attrs As attribute() - For Each scan As D2Chromatogram In gcxgc + For Each scan As Chromatogram2DScan In gcxgc vector = scan.chromatogram _ .Select(Function(d) d.Time) _ .JoinIterates(scan.chromatogram.Select(Function(d) d.Intensity)) _ @@ -168,7 +119,7 @@ Public Class D2Chromatogram : Implements IReadOnlyId, INamedValue ''' ''' the cdf file in mzkit format ''' - Public Shared Iterator Function DecodeCDF(file As Stream) As IEnumerable(Of D2Chromatogram) + Public Iterator Function DecodeCDF(file As Stream) As IEnumerable(Of Chromatogram2DScan) Using reader As New netCDFReader(file) Dim nscans As Integer = reader("nscans") Dim names As variable() = reader.variables @@ -181,7 +132,7 @@ Public Class D2Chromatogram : Implements IReadOnlyId, INamedValue Dim scan_time As Double = names(i).FindAttribute("scan_time").getObjectValue Dim intensity As Double = names(i).FindAttribute("intensity").getObjectValue - Yield New D2Chromatogram With { + Yield New Chromatogram2DScan With { .chromatogram = ticks, .intensity = intensity, .scan_time = scan_time @@ -189,9 +140,4 @@ Public Class D2Chromatogram : Implements IReadOnlyId, INamedValue Next End Using End Function - - - Public Function times() As Double() - Return chromatogram.Select(Function(t) t.Time).ToArray - End Function -End Class +End Module diff --git a/src/assembly/Comprehensive/GCxGC/Data.vb b/src/assembly/Comprehensive/GCxGC/Data.vb index df410f0601..f27cf4ad6c 100644 --- a/src/assembly/Comprehensive/GCxGC/Data.vb +++ b/src/assembly/Comprehensive/GCxGC/Data.vb @@ -63,9 +63,9 @@ Imports BioNovoGene.Analytical.MassSpectrometry.Math.Ms1 Public Module Data - Public Function ExtractXIC(mz As Double, mzdiff As Tolerance) As Func(Of ScanMS1, D2Chromatogram) + Public Function ExtractXIC(mz As Double, mzdiff As Tolerance) As Func(Of ScanMS1, Chromatogram2DScan) Return Function(d) - Return New D2Chromatogram With { + Return New Chromatogram2DScan With { .scan_time = d.rt, .intensity = d.GetIntensity(mz, mzdiff), .chromatogram = d.products _ @@ -81,13 +81,13 @@ Public Module Data End Function - Public Function ExtractTIC(rawdata As mzPack) As IEnumerable(Of D2Chromatogram) + Public Function ExtractTIC(rawdata As mzPack) As IEnumerable(Of Chromatogram2DScan) Return rawdata.MS.Select(Function(d1) d1.ExtractTIC) End Function - Public Function ExtractTIC(d As ScanMS1) As D2Chromatogram - Return New D2Chromatogram With { + Public Function ExtractTIC(d As ScanMS1) As Chromatogram2DScan + Return New Chromatogram2DScan With { .intensity = d.TIC, .scan_time = d.rt, .chromatogram = d.products _ diff --git a/src/assembly/Comprehensive/GCxGC/GC2Dimensional.vb b/src/assembly/Comprehensive/GCxGC/GC2Dimensional.vb index b1a11e689d..a4cd98b615 100644 --- a/src/assembly/Comprehensive/GCxGC/GC2Dimensional.vb +++ b/src/assembly/Comprehensive/GCxGC/GC2Dimensional.vb @@ -186,7 +186,7 @@ Public Module GC2Dimensional Public Function Demodulate2D(sig As ChromatogramTick(), modtime As Double, - Optional sampleRate As Double = Double.NaN) As D2Chromatogram() + Optional sampleRate As Double = Double.NaN) As Chromatogram2DScan() Dim size As Size = sig.Demodulate2DShape(modtime, sampleRate) Dim matrix = sig.Split(size.Width) _ @@ -238,10 +238,10 @@ Public Module GC2Dimensional End Function - Private Function scan1(t As ChromatogramTick()) As D2Chromatogram + Private Function scan1(t As ChromatogramTick()) As Chromatogram2DScan Dim t0 As Double = t(0).Time - Return New D2Chromatogram With { + Return New Chromatogram2DScan With { .scan_time = t0, .intensity = t.Sum(Function(i) i.Intensity), .chromatogram = t _ diff --git a/src/assembly/Comprehensive/MsImaging/MSIMeasurement.vb b/src/assembly/Comprehensive/MsImaging/MSIMeasurement.vb index 97d27f464a..b4d7aacc50 100644 --- a/src/assembly/Comprehensive/MsImaging/MSIMeasurement.vb +++ b/src/assembly/Comprehensive/MsImaging/MSIMeasurement.vb @@ -1,67 +1,64 @@ #Region "Microsoft.VisualBasic::71a9cd0f091f3397cd0fad24ccc9871f, assembly\Comprehensive\MsImaging\MSIMeasurement.vb" - ' Author: - ' - ' xieguigang (gg.xie@bionovogene.com, BioNovoGene Co., LTD.) - ' - ' Copyright (c) 2018 gg.xie@bionovogene.com, BioNovoGene Co., LTD. - ' - ' - ' MIT License - ' - ' - ' Permission is hereby granted, free of charge, to any person obtaining a copy - ' of this software and associated documentation files (the "Software"), to deal - ' in the Software without restriction, including without limitation the rights - ' to use, copy, modify, merge, publish, distribute, sublicense, and/or sell - ' copies of the Software, and to permit persons to whom the Software is - ' furnished to do so, subject to the following conditions: - ' - ' The above copyright notice and this permission notice shall be included in all - ' copies or substantial portions of the Software. - ' - ' THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR - ' IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, - ' FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE - ' AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER - ' LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, - ' OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE - ' SOFTWARE. - - - - ' /********************************************************************************/ - - ' Summaries: - - - ' Code Statistics: - - ' Total Lines: 98 - ' Code Lines: 75 (76.53%) - ' Comment Lines: 3 (3.06%) - ' - Xml Docs: 100.00% - ' - ' Blank Lines: 20 (20.41%) - ' File Size: 3.32 KB - - - ' Class MSIMeasurement - ' - ' Constructor: (+1 Overloads) Sub New - ' Function: GetCorrection, (+3 Overloads) Measure - ' - ' - ' /********************************************************************************/ +' Author: +' +' xieguigang (gg.xie@bionovogene.com, BioNovoGene Co., LTD.) +' +' Copyright (c) 2018 gg.xie@bionovogene.com, BioNovoGene Co., LTD. +' +' +' MIT License +' +' +' Permission is hereby granted, free of charge, to any person obtaining a copy +' of this software and associated documentation files (the "Software"), to deal +' in the Software without restriction, including without limitation the rights +' to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +' copies of the Software, and to permit persons to whom the Software is +' furnished to do so, subject to the following conditions: +' +' The above copyright notice and this permission notice shall be included in all +' copies or substantial portions of the Software. +' +' THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +' IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +' FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +' AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +' LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +' OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +' SOFTWARE. + + + +' /********************************************************************************/ + +' Summaries: + + +' Code Statistics: + +' Total Lines: 98 +' Code Lines: 75 (76.53%) +' Comment Lines: 3 (3.06%) +' - Xml Docs: 100.00% +' +' Blank Lines: 20 (20.41%) +' File Size: 3.32 KB + + +' Class MSIMeasurement +' +' Constructor: (+1 Overloads) Sub New +' Function: GetCorrection, (+3 Overloads) Measure +' +' +' /********************************************************************************/ #End Region -#If NET48 Then +Imports BioNovoGene.Analytical.MassSpectrometry.Assembly.mzData.mzWebCache Imports BioNovoGene.Analytical.MassSpectrometry.Assembly.ThermoRawFileReader Imports std = System.Math -#End If - -Imports BioNovoGene.Analytical.MassSpectrometry.Assembly.mzData.mzWebCache Namespace MsImaging @@ -126,8 +123,6 @@ Namespace MsImaging Return New MSIMeasurement(maxrt.Average, scans.Average, hasMs2:=scanMs2) End Function -#If NET48 Then - Public Shared Function Measure(raw As IEnumerable(Of MSFileReader), Optional scanMs2 As Boolean = False) As MSIMeasurement Dim scans As New List(Of Integer) Dim maxrt As New List(Of Double) @@ -150,7 +145,5 @@ Namespace MsImaging Return New MSIMeasurement(maxrt.Average, scans.Average, hasMs2:=scanMs2) End Function -#End If - End Class End Namespace diff --git a/src/assembly/Comprehensive/MsImaging/MsImagingRaw.vb b/src/assembly/Comprehensive/MsImaging/MsImagingRaw.vb index 050ff5219e..4ccd13741f 100644 --- a/src/assembly/Comprehensive/MsImaging/MsImagingRaw.vb +++ b/src/assembly/Comprehensive/MsImaging/MsImagingRaw.vb @@ -1,57 +1,57 @@ #Region "Microsoft.VisualBasic::429564ac2043fc1c86ec03dc05799e1c, assembly\Comprehensive\MsImaging\MsImagingRaw.vb" - ' Author: - ' - ' xieguigang (gg.xie@bionovogene.com, BioNovoGene Co., LTD.) - ' - ' Copyright (c) 2018 gg.xie@bionovogene.com, BioNovoGene Co., LTD. - ' - ' - ' MIT License - ' - ' - ' Permission is hereby granted, free of charge, to any person obtaining a copy - ' of this software and associated documentation files (the "Software"), to deal - ' in the Software without restriction, including without limitation the rights - ' to use, copy, modify, merge, publish, distribute, sublicense, and/or sell - ' copies of the Software, and to permit persons to whom the Software is - ' furnished to do so, subject to the following conditions: - ' - ' The above copyright notice and this permission notice shall be included in all - ' copies or substantial portions of the Software. - ' - ' THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR - ' IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, - ' FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE - ' AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER - ' LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, - ' OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE - ' SOFTWARE. - - - - ' /********************************************************************************/ - - ' Summaries: - - - ' Code Statistics: - - ' Total Lines: 245 - ' Code Lines: 187 (76.33%) - ' Comment Lines: 30 (12.24%) - ' - Xml Docs: 86.67% - ' - ' Blank Lines: 28 (11.43%) - ' File Size: 10.40 KB - - - ' Module MsImagingRaw - ' - ' Function: (+3 Overloads) GetMSIMetadata, MeasureRow, MSICombineRowScans, ParseRowNumber, Summary - ' - ' - ' /********************************************************************************/ +' Author: +' +' xieguigang (gg.xie@bionovogene.com, BioNovoGene Co., LTD.) +' +' Copyright (c) 2018 gg.xie@bionovogene.com, BioNovoGene Co., LTD. +' +' +' MIT License +' +' +' Permission is hereby granted, free of charge, to any person obtaining a copy +' of this software and associated documentation files (the "Software"), to deal +' in the Software without restriction, including without limitation the rights +' to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +' copies of the Software, and to permit persons to whom the Software is +' furnished to do so, subject to the following conditions: +' +' The above copyright notice and this permission notice shall be included in all +' copies or substantial portions of the Software. +' +' THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +' IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +' FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +' AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +' LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +' OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +' SOFTWARE. + + + +' /********************************************************************************/ + +' Summaries: + + +' Code Statistics: + +' Total Lines: 245 +' Code Lines: 187 (76.33%) +' Comment Lines: 30 (12.24%) +' - Xml Docs: 86.67% +' +' Blank Lines: 28 (11.43%) +' File Size: 10.40 KB + + +' Module MsImagingRaw +' +' Function: (+3 Overloads) GetMSIMetadata, MeasureRow, MSICombineRowScans, ParseRowNumber, Summary +' +' +' /********************************************************************************/ #End Region @@ -60,14 +60,19 @@ Imports System.Runtime.CompilerServices Imports BioNovoGene.Analytical.MassSpectrometry.Assembly.MarkupData.imzML Imports BioNovoGene.Analytical.MassSpectrometry.Assembly.mzData.mzWebCache Imports BioNovoGene.Analytical.MassSpectrometry.Math.Spectra +Imports BioNovoGene.Analytical.MassSpectrometry.MsImaging +Imports BioNovoGene.Analytical.MassSpectrometry.MsImaging.Reader Imports BioNovoGene.Analytical.MassSpectrometry.SingleCells.Deconvolute Imports Microsoft.VisualBasic.CommandLine.InteropService.Pipeline +Imports Microsoft.VisualBasic.ComponentModel.DataSourceModel Imports Microsoft.VisualBasic.ComponentModel.Ranges.Model +Imports Microsoft.VisualBasic.Imaging.BitmapImage Imports Microsoft.VisualBasic.Imaging.Math2D Imports Microsoft.VisualBasic.Language Imports Microsoft.VisualBasic.Linq Imports Microsoft.VisualBasic.Math.LinearAlgebra Imports Microsoft.VisualBasic.Math.Statistics.Linq +Imports Microsoft.VisualBasic.MIME.Html.CSS Imports Microsoft.VisualBasic.Scripting.Expressions Namespace MsImaging @@ -77,6 +82,102 @@ Namespace MsImaging '''
Public Module MsImagingRaw + ''' + ''' Try to save the tissue region data into mzPack rawdata file + ''' + ''' + ''' + ''' + + Public Function WriteRegionPoints(raw As mzPack, index As IEnumerable(Of NamedValue(Of Point))) As mzPack + Dim dimensionSize As Size = GetDimensionSize(raw) + Dim evalIndex As Func(Of Point, Integer) = Function(i) BitmapBuffer.GetIndex(i.X, i.Y, dimensionSize.Width, channels:=1) + Dim regions As Dictionary(Of String, Point()) = index _ + .GroupBy(Function(i) i.Name) _ + .ToDictionary(Function(region) region.Key, + Function(region) + Return region.Select(Function(i) i.Value).ToArray + End Function) + + Throw New NotImplementedException + End Function + + ''' + ''' + ''' + ''' + ''' + ''' + + Public Function PixelScanPadding(slide As mzPack, padding As Padding) As mzPack + Dim dims As Size = PixelReader.ReadDimensions(slide.MS.Select(Function(scan) scan.GetMSIPixel)) + Dim paddingData As ScanMS1() = slide.MS.PixelScanPadding(padding, dims).ToArray + + Return New mzPack With { + .MS = paddingData, + .Application = FileApplicationClass.MSImaging, + .Chromatogram = slide.Chromatogram, + .Scanners = slide.Scanners, + .source = slide.source, + .Thumbnail = slide.Thumbnail, + .metadata = slide.metadata, + .Annotations = slide.Annotations + } + End Function + + ''' + ''' reset sample position + ''' + ''' + ''' + ''' Add padding around the slide sample data + ''' + ''' + + Public Function Reset(raw As mzPack, padding As Padding) As mzPack + Dim rect As RectangleF = raw.Shape + Dim scans As New List(Of ScanMS1) + Dim pos As Point + Dim meta As Dictionary(Of String, String) + + For Each scan As ScanMS1 In raw.MS + pos = scan.GetMSIPixel + pos = New Point With { + .X = pos.X - rect.Left + padding.Left, + .Y = pos.Y - rect.Top + padding.Top + } + meta = New Dictionary(Of String, String)(scan.meta) + meta("x") = pos.X.ToString + meta("y") = pos.Y.ToString + + scans += New ScanMS1 With { + .BPC = scan.BPC, + .into = scan.into, + .mz = scan.mz, + .products = scan.products, + .rt = scan.rt, + .TIC = scan.TIC, + .scan_id = scan.scan_id, + .meta = meta + } + Next + + meta = raw.metadata + meta("width") = rect.Width + padding.Left + padding.Right + meta("height") = rect.Height + padding.Top + padding.Bottom + + Return New mzPack With { + .Application = FileApplicationClass.MSImaging, + .Chromatogram = raw.Chromatogram, + .MS = scans.ToArray, + .Scanners = raw.Scanners, + .source = $"reset({raw.source})", + .Thumbnail = Nothing, + .Annotations = raw.Annotations, + .metadata = meta + } + End Function + Public Function Summary(msidata As mzPack, Optional filter As Func(Of Integer, Integer, Boolean) = Nothing) As IEnumerable(Of iPixelIntensity) If filter Is Nothing Then diff --git a/src/assembly/Comprehensive/MsImaging/ScanTimeCorrection.vb b/src/assembly/Comprehensive/MsImaging/ScanTimeCorrection.vb index d7abf05952..f2b9e0b8b4 100644 --- a/src/assembly/Comprehensive/MsImaging/ScanTimeCorrection.vb +++ b/src/assembly/Comprehensive/MsImaging/ScanTimeCorrection.vb @@ -1,66 +1,67 @@ #Region "Microsoft.VisualBasic::4fdb1cdf96bbdb73c0b57fadebe1f764, assembly\Comprehensive\MsImaging\ScanTimeCorrection.vb" - ' Author: - ' - ' xieguigang (gg.xie@bionovogene.com, BioNovoGene Co., LTD.) - ' - ' Copyright (c) 2018 gg.xie@bionovogene.com, BioNovoGene Co., LTD. - ' - ' - ' MIT License - ' - ' - ' Permission is hereby granted, free of charge, to any person obtaining a copy - ' of this software and associated documentation files (the "Software"), to deal - ' in the Software without restriction, including without limitation the rights - ' to use, copy, modify, merge, publish, distribute, sublicense, and/or sell - ' copies of the Software, and to permit persons to whom the Software is - ' furnished to do so, subject to the following conditions: - ' - ' The above copyright notice and this permission notice shall be included in all - ' copies or substantial portions of the Software. - ' - ' THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR - ' IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, - ' FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE - ' AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER - ' LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, - ' OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE - ' SOFTWARE. - - - - ' /********************************************************************************/ - - ' Summaries: - - - ' Code Statistics: - - ' Total Lines: 56 - ' Code Lines: 29 (51.79%) - ' Comment Lines: 19 (33.93%) - ' - Xml Docs: 89.47% - ' - ' Blank Lines: 8 (14.29%) - ' File Size: 2.00 KB - - - ' Class ScanTimeCorrection - ' - ' Properties: pixels, pixelsTime, totalTime - ' - ' Constructor: (+1 Overloads) Sub New - ' Function: GetPixelPoint, GetPixelRow, GetPixelRowX - ' - ' - ' /********************************************************************************/ +' Author: +' +' xieguigang (gg.xie@bionovogene.com, BioNovoGene Co., LTD.) +' +' Copyright (c) 2018 gg.xie@bionovogene.com, BioNovoGene Co., LTD. +' +' +' MIT License +' +' +' Permission is hereby granted, free of charge, to any person obtaining a copy +' of this software and associated documentation files (the "Software"), to deal +' in the Software without restriction, including without limitation the rights +' to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +' copies of the Software, and to permit persons to whom the Software is +' furnished to do so, subject to the following conditions: +' +' The above copyright notice and this permission notice shall be included in all +' copies or substantial portions of the Software. +' +' THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +' IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +' FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +' AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +' LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +' OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +' SOFTWARE. + + + +' /********************************************************************************/ + +' Summaries: + + +' Code Statistics: + +' Total Lines: 56 +' Code Lines: 29 (51.79%) +' Comment Lines: 19 (33.93%) +' - Xml Docs: 89.47% +' +' Blank Lines: 8 (14.29%) +' File Size: 2.00 KB + + +' Class ScanTimeCorrection +' +' Properties: pixels, pixelsTime, totalTime +' +' Constructor: (+1 Overloads) Sub New +' Function: GetPixelPoint, GetPixelRow, GetPixelRowX +' +' +' /********************************************************************************/ #End Region Imports System.Drawing Imports System.Runtime.CompilerServices Imports BioNovoGene.Analytical.MassSpectrometry.Assembly.mzData.mzWebCache +Imports Microsoft.VisualBasic.Data.GraphTheory.GridGraph Imports Microsoft.VisualBasic.Imaging.BitmapImage Namespace MsImaging @@ -112,5 +113,65 @@ Namespace MsImaging Public Overrides Function GetPixelRowX(scanMs1 As ScanMS1) As Integer Return GetPixelRow(scanMs1.rt) End Function + + ''' + ''' make bugs fixed for RT pixel correction + ''' + ''' + ''' + ''' set this parameter value to nothing will mute the log message echo. + ''' + ''' + Public Shared Function ScanMeltdown(MSI As mzPack, + Optional gridSize As Integer = 2, + Optional println As Action(Of String) = Nothing) As mzPack + + Dim graph = Grid(Of ScanMS1).Create(MSI.MS, Function(d) d.GetMSIPixel) + Dim scans As New List(Of ScanMS1) + Dim dims As New Size(graph.width, graph.height) + Dim pixel As ScanMS1 + + If println Is Nothing Then + println = + Sub() + + End Sub + Else + Call println("make bugs fixed for RT pixel correction!") + End If + + For i As Integer = 1 To dims.Width + For j As Integer = 1 To dims.Height + pixel = graph.GetData(i, j) + + If pixel Is Nothing Then + For xi As Integer = -1 To -gridSize Step -1 + pixel = graph.GetData(i + xi, j) + + If Not pixel Is Nothing Then + Exit For + End If + Next + End If + + If Not pixel Is Nothing Then + scans.Add(pixel) + Else + Call println($"Missing pixel data at [{i}, {j}]!") + End If + Next + Next + + Return New mzPack With { + .Application = FileApplicationClass.MSImaging, + .Chromatogram = MSI.Chromatogram, + .MS = scans.ToArray, + .Scanners = MSI.Scanners, + .source = MSI.source, + .Thumbnail = MSI.Thumbnail, + .Annotations = MSI.Annotations, + .metadata = MSI.metadata + } + End Function End Class End Namespace diff --git a/src/mzmath/GCxGC/ChromatogramMesh.vb b/src/mzmath/GCxGC/ChromatogramMesh.vb new file mode 100644 index 0000000000..93e7f53164 --- /dev/null +++ b/src/mzmath/GCxGC/ChromatogramMesh.vb @@ -0,0 +1,68 @@ +Imports System.Runtime.CompilerServices +Imports BioNovoGene.Analytical.MassSpectrometry.Math.Chromatogram +Imports Microsoft.VisualBasic.ComponentModel.Collection.Generic +Imports Microsoft.VisualBasic.ComponentModel.Ranges.Model +Imports Microsoft.VisualBasic.Scripting.Expressions + +''' +''' A 2d chromatogram mesh grid data that consists with the GCxGC chromatogram data +''' +Public Class ChromatogramMesh + + Public Property scan2D As Chromatogram2DScan() + +End Class + +Public Class Chromatogram2DScan : Implements IReadOnlyId, INamedValue + Public Property scan_time As Double + Public Property intensity As Double + Public Property scan_id As String Implements INamedValue.Key, IReadOnlyId.Identity + + ''' + ''' chromatogram data 2d + ''' + ''' + Public Property chromatogram As ChromatogramTick() + + Default Public ReadOnly Property getTick(i As DoubleRange) As ChromatogramTick() + Get + Return chromatogram.Where(Function(a) i.IsInside(a.Time)).ToArray + End Get + End Property + + Default Public ReadOnly Property getTick(i As Integer) As ChromatogramTick + + Get + Return _chromatogram(i) + End Get + End Property + + Public ReadOnly Property size As Integer + + Get + Return chromatogram.Length + End Get + End Property + + Sub New() + End Sub + + Sub New(t1 As Double) + scan_time = t1 + End Sub + + Sub New(t1 As Double, id As String) + scan_id = id + scan_time = t1 + End Sub + + + Public Function times() As Double() + Return chromatogram.Select(Function(t) t.Time).ToArray + End Function + + + Public Overrides Function ToString() As String + Return $"{intensity.ToString("G3")}@{scan_time.ToString("F2")}" + End Function +End Class \ No newline at end of file diff --git a/src/mzmath/TargetedMetabolomics/Targetted.NET5.vbproj b/src/mzmath/TargetedMetabolomics/Targetted.NET5.vbproj index 8f3d1ac4a0..bc3cb2837b 100644 --- a/src/mzmath/TargetedMetabolomics/Targetted.NET5.vbproj +++ b/src/mzmath/TargetedMetabolomics/Targetted.NET5.vbproj @@ -118,7 +118,6 @@ - diff --git a/src/mzmath/ms2_math-core/Spectra/Models/Xml/AlignmentOutput.vb b/src/mzmath/ms2_math-core/Spectra/Models/Xml/AlignmentOutput.vb index 7feb4451d9..08c1b89697 100644 --- a/src/mzmath/ms2_math-core/Spectra/Models/Xml/AlignmentOutput.vb +++ b/src/mzmath/ms2_math-core/Spectra/Models/Xml/AlignmentOutput.vb @@ -66,11 +66,33 @@ Imports std = System.Math Namespace Spectra.Xml + ''' + ''' the spectrum similarity comparision result object + ''' + ''' + ''' contains the score and spectrum fragment alignment details result data. + ''' Public Class AlignmentOutput + ''' + ''' the forward cosine score + ''' + ''' Public Property forward As Double + ''' + ''' the reverse cosine score + ''' + ''' Public Property reverse As Double + ''' + ''' the jaccard index between the fragment set of query vs subject + ''' + ''' Public Property jaccard As Double + ''' + ''' the spectrum entropy similarity + ''' + ''' Public Property entropy As Double Public ReadOnly Property mirror As Double diff --git a/src/visualize/MsImaging/Analysis/GridScanner.vb b/src/visualize/MsImaging/Analysis/GridScanner.vb index ef1b2dcaf3..e51dd4836f 100644 --- a/src/visualize/MsImaging/Analysis/GridScanner.vb +++ b/src/visualize/MsImaging/Analysis/GridScanner.vb @@ -191,7 +191,7 @@ Public Module GridScanner ''' ''' - Public Function IonColocalization(raw As mzPack, + Public Function IonColocalization(raw As IMZPack, Optional grid_width As Integer = 5, Optional grid_height As Integer = 5, Optional repeats As Integer = 3, diff --git a/src/visualize/MsImaging/Analysis/SpatialIonStats.vb b/src/visualize/MsImaging/Analysis/SpatialIonStats.vb index 06234c2761..262a57367f 100644 --- a/src/visualize/MsImaging/Analysis/SpatialIonStats.vb +++ b/src/visualize/MsImaging/Analysis/SpatialIonStats.vb @@ -1,60 +1,60 @@ #Region "Microsoft.VisualBasic::5974ecf93ca26e3014e220103093bdd8, visualize\MsImaging\Analysis\SpatialIonStats.vb" - ' Author: - ' - ' xieguigang (gg.xie@bionovogene.com, BioNovoGene Co., LTD.) - ' - ' Copyright (c) 2018 gg.xie@bionovogene.com, BioNovoGene Co., LTD. - ' - ' - ' MIT License - ' - ' - ' Permission is hereby granted, free of charge, to any person obtaining a copy - ' of this software and associated documentation files (the "Software"), to deal - ' in the Software without restriction, including without limitation the rights - ' to use, copy, modify, merge, publish, distribute, sublicense, and/or sell - ' copies of the Software, and to permit persons to whom the Software is - ' furnished to do so, subject to the following conditions: - ' - ' The above copyright notice and this permission notice shall be included in all - ' copies or substantial portions of the Software. - ' - ' THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR - ' IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, - ' FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE - ' AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER - ' LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, - ' OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE - ' SOFTWARE. - - - - ' /********************************************************************************/ - - ' Summaries: - - - ' Code Statistics: - - ' Total Lines: 112 - ' Code Lines: 77 (68.75%) - ' Comment Lines: 27 (24.11%) - ' - Xml Docs: 85.19% - ' - ' Blank Lines: 8 (7.14%) - ' File Size: 4.94 KB - - - ' Class SpatialIonStats - ' - ' Function: (+3 Overloads) DoStat - ' - ' /********************************************************************************/ +' Author: +' +' xieguigang (gg.xie@bionovogene.com, BioNovoGene Co., LTD.) +' +' Copyright (c) 2018 gg.xie@bionovogene.com, BioNovoGene Co., LTD. +' +' +' MIT License +' +' +' Permission is hereby granted, free of charge, to any person obtaining a copy +' of this software and associated documentation files (the "Software"), to deal +' in the Software without restriction, including without limitation the rights +' to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +' copies of the Software, and to permit persons to whom the Software is +' furnished to do so, subject to the following conditions: +' +' The above copyright notice and this permission notice shall be included in all +' copies or substantial portions of the Software. +' +' THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +' IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +' FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +' AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +' LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +' OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +' SOFTWARE. + + + +' /********************************************************************************/ + +' Summaries: + + +' Code Statistics: + +' Total Lines: 112 +' Code Lines: 77 (68.75%) +' Comment Lines: 27 (24.11%) +' - Xml Docs: 85.19% +' +' Blank Lines: 8 (7.14%) +' File Size: 4.94 KB + + +' Class SpatialIonStats +' +' Function: (+3 Overloads) DoStat +' +' /********************************************************************************/ #End Region -Imports BioNovoGene.Analytical.MassSpectrometry.Assembly +Imports BioNovoGene.Analytical.MassSpectrometry.Assembly.mzData.mzWebCache Imports BioNovoGene.Analytical.MassSpectrometry.Math.Spectra Imports BioNovoGene.Analytical.MassSpectrometry.MsImaging.Pixel Imports BioNovoGene.Analytical.MassSpectrometry.MsImaging.StatsMath @@ -128,7 +128,7 @@ Public Class SpatialIonStats ''' the grid size for evaluate the density value ''' ''' - Public Shared Function DoStat(raw As mzPack, + Public Shared Function DoStat(raw As IMZPack, Optional nsize As Integer = 5, Optional da As Double = 0.05, Optional parallel As Boolean = False) As IEnumerable(Of IonStat) diff --git a/src/visualize/MsImaging/Drawer.vb b/src/visualize/MsImaging/Drawer.vb index 50bb955ea2..ed5c72f84e 100644 --- a/src/visualize/MsImaging/Drawer.vb +++ b/src/visualize/MsImaging/Drawer.vb @@ -1,63 +1,63 @@ #Region "Microsoft.VisualBasic::bb499fee4f1308b5f978080e219bd854, visualize\MsImaging\Drawer.vb" - ' Author: - ' - ' xieguigang (gg.xie@bionovogene.com, BioNovoGene Co., LTD.) - ' - ' Copyright (c) 2018 gg.xie@bionovogene.com, BioNovoGene Co., LTD. - ' - ' - ' MIT License - ' - ' - ' Permission is hereby granted, free of charge, to any person obtaining a copy - ' of this software and associated documentation files (the "Software"), to deal - ' in the Software without restriction, including without limitation the rights - ' to use, copy, modify, merge, publish, distribute, sublicense, and/or sell - ' copies of the Software, and to permit persons to whom the Software is - ' furnished to do so, subject to the following conditions: - ' - ' The above copyright notice and this permission notice shall be included in all - ' copies or substantial portions of the Software. - ' - ' THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR - ' IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, - ' FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE - ' AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER - ' LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, - ' OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE - ' SOFTWARE. - - - - ' /********************************************************************************/ - - ' Summaries: - - - ' Code Statistics: - - ' Total Lines: 365 - ' Code Lines: 221 (60.55%) - ' Comment Lines: 95 (26.03%) - ' - Xml Docs: 87.37% - ' - ' Blank Lines: 49 (13.42%) - ' File Size: 14.53 KB - - - ' Class Drawer - ' - ' Properties: dimension, pixelReader - ' - ' Constructor: (+4 Overloads) Sub New - ' - ' Function: (+2 Overloads) DrawLayer, GetPixelsMatrix, (+2 Overloads) LoadPixels, ReadXY, RenderSummaryLayer - ' (+2 Overloads) ScaleLayer, ScalePixels, ShowSummaryRendering - ' - ' Sub: (+2 Overloads) Dispose - ' - ' /********************************************************************************/ +' Author: +' +' xieguigang (gg.xie@bionovogene.com, BioNovoGene Co., LTD.) +' +' Copyright (c) 2018 gg.xie@bionovogene.com, BioNovoGene Co., LTD. +' +' +' MIT License +' +' +' Permission is hereby granted, free of charge, to any person obtaining a copy +' of this software and associated documentation files (the "Software"), to deal +' in the Software without restriction, including without limitation the rights +' to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +' copies of the Software, and to permit persons to whom the Software is +' furnished to do so, subject to the following conditions: +' +' The above copyright notice and this permission notice shall be included in all +' copies or substantial portions of the Software. +' +' THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +' IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +' FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +' AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +' LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +' OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +' SOFTWARE. + + + +' /********************************************************************************/ + +' Summaries: + + +' Code Statistics: + +' Total Lines: 365 +' Code Lines: 221 (60.55%) +' Comment Lines: 95 (26.03%) +' - Xml Docs: 87.37% +' +' Blank Lines: 49 (13.42%) +' File Size: 14.53 KB + + +' Class Drawer +' +' Properties: dimension, pixelReader +' +' Constructor: (+4 Overloads) Sub New +' +' Function: (+2 Overloads) DrawLayer, GetPixelsMatrix, (+2 Overloads) LoadPixels, ReadXY, RenderSummaryLayer +' (+2 Overloads) ScaleLayer, ScalePixels, ShowSummaryRendering +' +' Sub: (+2 Overloads) Dispose +' +' /********************************************************************************/ #End Region @@ -74,6 +74,8 @@ Imports BioNovoGene.Analytical.MassSpectrometry.MsImaging.Reader Imports Microsoft.VisualBasic.Imaging.Driver Imports Microsoft.VisualBasic.Linq Imports Microsoft.VisualBasic.Math +Imports BioNovoGene.Analytical.MassSpectrometry.Assembly.mzData.mzWebCache + #If NET48 Then Imports Microsoft.VisualBasic.Drawing @@ -141,7 +143,8 @@ Public Class Drawer : Implements IDisposable If file.ExtensionSuffix("imzML") Then pixelReader = New ReadIbd(imzML:=file, memoryCache:=memoryCache) ElseIf file.ExtensionSuffix("mzpack") Then - pixelReader = New ReadRawPack(mzpack:=file, verbose:=verbose) + ' pixelReader = New ReadRawPack(mzpack:=file, verbose:=verbose) + Throw New NotSupportedException($"Create ms-imaging rendering canvas from read mzPack rawdata file is not supported.") Else Throw New InvalidProgramException($"unsupported file type: {file.FileName}") End If @@ -150,9 +153,11 @@ Public Class Drawer : Implements IDisposable ''' ''' Create render from an in-memory dataset ''' - ''' + ''' + ''' An abstract interface of the in-memory mzPack data object + ''' ''' - Sub New(mzpack As mzPack, Optional verbose As Boolean = True) + Sub New(mzpack As IMZPack, Optional verbose As Boolean = True) pixelReader = New ReadRawPack(mzpack, verbose) End Sub diff --git a/src/visualize/MsImaging/Extensions.vb b/src/visualize/MsImaging/Extensions.vb index 43f7d00a36..6c1d83091a 100644 --- a/src/visualize/MsImaging/Extensions.vb +++ b/src/visualize/MsImaging/Extensions.vb @@ -57,17 +57,13 @@ Imports System.Drawing Imports System.Runtime.CompilerServices -Imports BioNovoGene.Analytical.MassSpectrometry.Assembly Imports BioNovoGene.Analytical.MassSpectrometry.Assembly.MarkupData.imzML Imports BioNovoGene.Analytical.MassSpectrometry.Assembly.mzData.mzWebCache -Imports BioNovoGene.Analytical.MassSpectrometry.MsImaging.Reader Imports Microsoft.VisualBasic.ComponentModel.Collection Imports Microsoft.VisualBasic.ComponentModel.DataSourceModel -Imports Microsoft.VisualBasic.Data.GraphTheory.GridGraph Imports Microsoft.VisualBasic.DataMining.DensityQuery Imports Microsoft.VisualBasic.Imaging.Drawing2D.HeatMap Imports Microsoft.VisualBasic.Imaging.Math2D -Imports Microsoft.VisualBasic.Language Imports Microsoft.VisualBasic.Linq Imports Microsoft.VisualBasic.Math.Quantile Imports Microsoft.VisualBasic.MIME.Html.CSS @@ -76,59 +72,6 @@ Imports Point = System.Drawing.Point Public Module Extensions - ''' - ''' reset sample position - ''' - ''' - ''' - ''' Add padding around the slide sample data - ''' - ''' - - Public Function Reset(raw As mzPack, padding As Padding) As mzPack - Dim rect As RectangleF = raw.Shape - Dim scans As New List(Of ScanMS1) - Dim pos As Point - Dim meta As Dictionary(Of String, String) - - For Each scan As ScanMS1 In raw.MS - pos = scan.GetMSIPixel - pos = New Point With { - .X = pos.X - rect.Left + padding.Left, - .Y = pos.Y - rect.Top + padding.Top - } - meta = New Dictionary(Of String, String)(scan.meta) - meta("x") = pos.X.ToString - meta("y") = pos.Y.ToString - - scans += New ScanMS1 With { - .BPC = scan.BPC, - .into = scan.into, - .mz = scan.mz, - .products = scan.products, - .rt = scan.rt, - .TIC = scan.TIC, - .scan_id = scan.scan_id, - .meta = meta - } - Next - - meta = raw.metadata - meta("width") = rect.Width + padding.Left + padding.Right - meta("height") = rect.Height + padding.Top + padding.Bottom - - Return New mzPack With { - .Application = FileApplicationClass.MSImaging, - .Chromatogram = raw.Chromatogram, - .MS = scans.ToArray, - .Scanners = raw.Scanners, - .source = $"reset({raw.source})", - .Thumbnail = Nothing, - .Annotations = raw.Annotations, - .metadata = meta - } - End Function - ''' ''' get pixels boundary of the MSImaging ''' @@ -138,7 +81,7 @@ Public Module Extensions ''' location and size ''' - Public Function Shape(raw As mzPack) As RectangleF + Public Function Shape(raw As IMZPack) As RectangleF Dim allPixels As Point() = raw.MS.Select(Function(scan) scan.GetMSIPixel).ToArray Dim polygonShape As New Polygon2D(allPixels) Dim rect = polygonShape.GetRectangle @@ -168,33 +111,10 @@ Public Module Extensions End Function) End Function - ''' - ''' - ''' - ''' - ''' - ''' - - Public Function PixelScanPadding(slide As mzPack, padding As Padding) As mzPack - Dim dims As Size = PixelReader.ReadDimensions(slide.MS.Select(Function(scan) scan.GetMSIPixel)) - Dim paddingData As ScanMS1() = slide.MS.PixelScanPadding(padding, dims).ToArray - - Return New mzPack With { - .MS = paddingData, - .Application = FileApplicationClass.MSImaging, - .Chromatogram = slide.Chromatogram, - .Scanners = slide.Scanners, - .source = slide.source, - .Thumbnail = slide.Thumbnail, - .metadata = slide.metadata, - .Annotations = slide.Annotations - } - End Function - - Private Iterator Function PixelScanPadding(raw As IEnumerable(Of ScanMS1), - padding As Padding, - dims As Size) As IEnumerable(Of ScanMS1) + Public Iterator Function PixelScanPadding(raw As IEnumerable(Of ScanMS1), + padding As Padding, + dims As Size) As IEnumerable(Of ScanMS1) Dim marginRight As Integer = dims.Width - padding.Right Dim marginLeft As Integer = padding.Left @@ -249,67 +169,6 @@ Public Module Extensions Next End Function - ''' - ''' make bugs fixed for RT pixel correction - ''' - ''' - ''' - ''' set this parameter value to nothing will mute the log message echo. - ''' - ''' - - Public Function ScanMeltdown(MSI As mzPack, - Optional gridSize As Integer = 2, - Optional println As Action(Of String) = Nothing) As mzPack - - Dim graph = Grid(Of ScanMS1).Create(MSI.MS, Function(d) d.GetMSIPixel) - Dim scans As New List(Of ScanMS1) - Dim dims As New Size(graph.width, graph.height) - Dim pixel As ScanMS1 - - If println Is Nothing Then - println = - Sub() - - End Sub - Else - Call println("make bugs fixed for RT pixel correction!") - End If - - For i As Integer = 1 To dims.Width - For j As Integer = 1 To dims.Height - pixel = graph.GetData(i, j) - - If pixel Is Nothing Then - For xi As Integer = -1 To -gridSize Step -1 - pixel = graph.GetData(i + xi, j) - - If Not pixel Is Nothing Then - Exit For - End If - Next - End If - - If Not pixel Is Nothing Then - scans.Add(pixel) - Else - Call println($"Missing pixel data at [{i}, {j}]!") - End If - Next - Next - - Return New mzPack With { - .Application = FileApplicationClass.MSImaging, - .Chromatogram = MSI.Chromatogram, - .MS = scans.ToArray, - .Scanners = MSI.Scanners, - .source = MSI.source, - .Thumbnail = MSI.Thumbnail, - .Annotations = MSI.Annotations, - .metadata = MSI.metadata - } - End Function - ''' ''' cast ion layer data to raster matrix object ''' diff --git a/src/visualize/MsImaging/FeatureRegions.vb b/src/visualize/MsImaging/FeatureRegions.vb index 3326ed4416..b47543472a 100644 --- a/src/visualize/MsImaging/FeatureRegions.vb +++ b/src/visualize/MsImaging/FeatureRegions.vb @@ -1,56 +1,56 @@ #Region "Microsoft.VisualBasic::da9c4dc46354b0be9a308cea2592ecb3, visualize\MsImaging\FeatureRegions.vb" - ' Author: - ' - ' xieguigang (gg.xie@bionovogene.com, BioNovoGene Co., LTD.) - ' - ' Copyright (c) 2018 gg.xie@bionovogene.com, BioNovoGene Co., LTD. - ' - ' - ' MIT License - ' - ' - ' Permission is hereby granted, free of charge, to any person obtaining a copy - ' of this software and associated documentation files (the "Software"), to deal - ' in the Software without restriction, including without limitation the rights - ' to use, copy, modify, merge, publish, distribute, sublicense, and/or sell - ' copies of the Software, and to permit persons to whom the Software is - ' furnished to do so, subject to the following conditions: - ' - ' The above copyright notice and this permission notice shall be included in all - ' copies or substantial portions of the Software. - ' - ' THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR - ' IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, - ' FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE - ' AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER - ' LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, - ' OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE - ' SOFTWARE. - - - - ' /********************************************************************************/ - - ' Summaries: - - - ' Code Statistics: - - ' Total Lines: 93 - ' Code Lines: 77 (82.80%) - ' Comment Lines: 5 (5.38%) - ' - Xml Docs: 100.00% - ' - ' Blank Lines: 11 (11.83%) - ' File Size: 3.95 KB - - - ' Module FeatureRegions - ' - ' Function: GetDimensionSize, TakeRegion, TrimRegion, WriteRegionPoints - ' - ' /********************************************************************************/ +' Author: +' +' xieguigang (gg.xie@bionovogene.com, BioNovoGene Co., LTD.) +' +' Copyright (c) 2018 gg.xie@bionovogene.com, BioNovoGene Co., LTD. +' +' +' MIT License +' +' +' Permission is hereby granted, free of charge, to any person obtaining a copy +' of this software and associated documentation files (the "Software"), to deal +' in the Software without restriction, including without limitation the rights +' to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +' copies of the Software, and to permit persons to whom the Software is +' furnished to do so, subject to the following conditions: +' +' The above copyright notice and this permission notice shall be included in all +' copies or substantial portions of the Software. +' +' THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +' IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +' FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +' AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +' LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +' OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +' SOFTWARE. + + + +' /********************************************************************************/ + +' Summaries: + + +' Code Statistics: + +' Total Lines: 93 +' Code Lines: 77 (82.80%) +' Comment Lines: 5 (5.38%) +' - Xml Docs: 100.00% +' +' Blank Lines: 11 (11.83%) +' File Size: 3.95 KB + + +' Module FeatureRegions +' +' Function: GetDimensionSize, TakeRegion, TrimRegion, WriteRegionPoints +' +' /********************************************************************************/ #End Region @@ -58,6 +58,7 @@ Imports System.Drawing Imports System.Runtime.CompilerServices Imports BioNovoGene.Analytical.MassSpectrometry.Assembly Imports BioNovoGene.Analytical.MassSpectrometry.Assembly.MarkupData.imzML +Imports BioNovoGene.Analytical.MassSpectrometry.Assembly.mzData.mzWebCache Imports Microsoft.VisualBasic.ComponentModel.Collection Imports Microsoft.VisualBasic.ComponentModel.DataSourceModel Imports Microsoft.VisualBasic.Imaging.BitmapImage @@ -66,27 +67,13 @@ Imports Microsoft.VisualBasic.Linq Public Module FeatureRegions - - Public Function WriteRegionPoints(raw As mzPack, index As IEnumerable(Of NamedValue(Of Point))) As mzPack - Dim dimensionSize As Size = GetDimensionSize(raw) - Dim evalIndex As Func(Of Point, Integer) = Function(i) BitmapBuffer.GetIndex(i.X, i.Y, dimensionSize.Width, channels:=1) - Dim regions As Dictionary(Of String, Point()) = index _ - .GroupBy(Function(i) i.Name) _ - .ToDictionary(Function(region) region.Key, - Function(region) - Return region.Select(Function(i) i.Value).ToArray - End Function) - - Throw New NotImplementedException - End Function - ''' ''' get the dimension size of the ms-imaging canvas ''' ''' ''' - Public Function GetDimensionSize(raw As mzPack) As Size + Public Function GetDimensionSize(raw As IMZPack) As Size Dim allPixels As Point() = raw.MS.Select(Function(p) p.GetMSIPixel).ToArray Dim width As Integer = Aggregate pi As Point In allPixels Into Max(pi.X) Dim height As Integer = Aggregate pi As Point In allPixels Into Max(pi.Y) diff --git a/src/visualize/MsImaging/Layer/LayerHelpers.vb b/src/visualize/MsImaging/Layer/LayerHelpers.vb index 7249ebbbec..51bf472742 100644 --- a/src/visualize/MsImaging/Layer/LayerHelpers.vb +++ b/src/visualize/MsImaging/Layer/LayerHelpers.vb @@ -56,7 +56,6 @@ Imports System.Drawing Imports System.Runtime.CompilerServices -Imports BioNovoGene.Analytical.MassSpectrometry.Assembly Imports BioNovoGene.Analytical.MassSpectrometry.Assembly.mzData.mzWebCache Imports BioNovoGene.Analytical.MassSpectrometry.Math.Ms1 Imports BioNovoGene.Analytical.MassSpectrometry.Math.Spectra @@ -70,7 +69,7 @@ Imports Microsoft.VisualBasic.Language Imports Microsoft.VisualBasic.Linq Imports Microsoft.VisualBasic.Math Imports Microsoft.VisualBasic.Math.Statistics.Linq -Imports stdNum = System.Math +Imports std = System.Math Public Module LayerHelpers @@ -83,7 +82,7 @@ Public Module LayerHelpers ''' a collection of m/z tagged density value ''' - Public Iterator Function GetMSIIons(raw As mzPack, + Public Iterator Function GetMSIIons(raw As IMZPack, Optional mzdiff As Tolerance = Nothing, Optional gridSize As Integer = 5, Optional qcut As Double = 0.05, @@ -122,7 +121,7 @@ Public Module LayerHelpers j = 0 info = $"({CInt(100 * i / allMz.Length)}%) {Val(allMz(i).name).ToString("F4")}" - Call RunSlavePipeline.SendProgress(stdNum.Round(i / allMz.Length, 2), info) + Call RunSlavePipeline.SendProgress(std.Round(i / allMz.Length, 2), info) End If Next End Function diff --git a/src/visualize/MsImaging/MsImaging.NET5.vbproj b/src/visualize/MsImaging/MsImaging.NET5.vbproj index f898a2255d..c886d98fef 100644 --- a/src/visualize/MsImaging/MsImaging.NET5.vbproj +++ b/src/visualize/MsImaging/MsImaging.NET5.vbproj @@ -241,6 +241,7 @@ + @@ -251,7 +252,6 @@ - diff --git a/src/visualize/MsImaging/Reader/PixelScan/InMemoryVectorPixel.vb b/src/visualize/MsImaging/Reader/PixelScan/InMemoryVectorPixel.vb index 2f6af391a6..6e07a3f91f 100644 --- a/src/visualize/MsImaging/Reader/PixelScan/InMemoryVectorPixel.vb +++ b/src/visualize/MsImaging/Reader/PixelScan/InMemoryVectorPixel.vb @@ -123,8 +123,8 @@ Namespace Pixel Sub New(scan As ScanMS1) Call Me.New(scan.scan_id, scan.meta!x, scan.meta!y, scan.mz, scan.into) - If scan.hasMetaKeys(mzStreamWriter.SampleMetaName) Then - sampleTag = scan.meta(mzStreamWriter.SampleMetaName) + If scan.hasMetaKeys(mzPackPixel.SampleMetaName) Then + sampleTag = scan.meta(mzPackPixel.SampleMetaName) End If End Sub diff --git a/src/visualize/MsImaging/Reader/PixelScan/mzPackPixel.vb b/src/visualize/MsImaging/Reader/PixelScan/mzPackPixel.vb index d5a312c753..252594f626 100644 --- a/src/visualize/MsImaging/Reader/PixelScan/mzPackPixel.vb +++ b/src/visualize/MsImaging/Reader/PixelScan/mzPackPixel.vb @@ -106,10 +106,12 @@ Namespace Pixel End Get End Property + Public Const SampleMetaName As String = "sample" + Public Overrides ReadOnly Property sampleTag As String Get - If scan.hasMetaKeys(mzStreamWriter.SampleMetaName) Then - Return scan.meta(mzStreamWriter.SampleMetaName) + If scan.hasMetaKeys(SampleMetaName) Then + Return scan.meta(SampleMetaName) Else Return Nothing End If diff --git a/src/visualize/MsImaging/Reader/ReadRawPack.vb b/src/visualize/MsImaging/Reader/ReadRawPack.vb index 29b7e3a350..4c3e6cac5a 100644 --- a/src/visualize/MsImaging/Reader/ReadRawPack.vb +++ b/src/visualize/MsImaging/Reader/ReadRawPack.vb @@ -89,7 +89,7 @@ Namespace Reader ''' Dim pixels As Dictionary(Of String, mzPackPixel()) - Sub New(mzpack As Assembly.mzPack, Optional verbose As Boolean = True) + Sub New(mzpack As IMZPack, Optional verbose As Boolean = True) Call mzpack.MS _ .Select(Function(pixel) Return New mzPackPixel(pixel) @@ -104,18 +104,19 @@ Namespace Reader Call ReadDimensions(mzpack:=Nothing, verbose) End Sub - Sub New(mzpack As String, Optional verbose As Boolean = True) - Using file As Stream = mzpack.Open(FileMode.Open, doClear:=False, [readOnly]:=True) - Call Assembly.mzPack _ - .ReadAll(file).MS _ - .Select(Function(pixel) - Return New mzPackPixel(pixel) - End Function) _ - .DoCall(Sub(ls) loadPixelsArray(ls, verbose)) - - Call ReadDimensions(mzpack:=Nothing, verbose) - End Using - End Sub + ' load from mzpack rawdata file + 'Sub New(mzpack As String, Optional verbose As Boolean = True) + ' Using file As Stream = mzpack.Open(FileMode.Open, doClear:=False, [readOnly]:=True) + ' Call Assembly.mzPack _ + ' .ReadAll(file).MS _ + ' .Select(Function(pixel) + ' Return New mzPackPixel(pixel) + ' End Function) _ + ' .DoCall(Sub(ls) loadPixelsArray(ls, verbose)) + + ' Call ReadDimensions(mzpack:=Nothing, verbose) + ' End Using + 'End Sub Sub New(pixels As IEnumerable(Of mzPackPixel), MsiDim As Size, resolution As Double, Optional verbose As Boolean = True) Me.dimension = MsiDim @@ -159,7 +160,7 @@ Namespace Reader ''' the required mzpack object could be nothing ''' ''' - Private Overloads Sub ReadDimensions(mzpack As mzPack, verbose As Boolean) + Private Overloads Sub ReadDimensions(mzpack As IMZPack, verbose As Boolean) Dim metadata As Dictionary(Of String, String) Dim polygon As New Polygon2D(pixels.Select(Function(pr) pr.Value).IteratesALL.Select(Function(p) New Point(p.X, p.Y))) diff --git a/src/visualize/TissueMorphology/TissueMorphology.vbproj b/src/visualize/TissueMorphology/TissueMorphology.vbproj index 5064d4a5fa..5ec1a6e6e3 100644 --- a/src/visualize/TissueMorphology/TissueMorphology.vbproj +++ b/src/visualize/TissueMorphology/TissueMorphology.vbproj @@ -90,7 +90,6 @@ - diff --git a/src/visualize/plot/GCxGC/GCxGCHeatMap.vb b/src/visualize/plot/GCxGC/GCxGCHeatMap.vb index 3e6c0f7779..af3bc377d8 100644 --- a/src/visualize/plot/GCxGC/GCxGCHeatMap.vb +++ b/src/visualize/plot/GCxGC/GCxGCHeatMap.vb @@ -1,65 +1,65 @@ #Region "Microsoft.VisualBasic::b81c88361889c0fc4305f9df04014bd8, visualize\plot\GCxGC\GCxGCHeatMap.vb" - ' Author: - ' - ' xieguigang (gg.xie@bionovogene.com, BioNovoGene Co., LTD.) - ' - ' Copyright (c) 2018 gg.xie@bionovogene.com, BioNovoGene Co., LTD. - ' - ' - ' MIT License - ' - ' - ' Permission is hereby granted, free of charge, to any person obtaining a copy - ' of this software and associated documentation files (the "Software"), to deal - ' in the Software without restriction, including without limitation the rights - ' to use, copy, modify, merge, publish, distribute, sublicense, and/or sell - ' copies of the Software, and to permit persons to whom the Software is - ' furnished to do so, subject to the following conditions: - ' - ' The above copyright notice and this permission notice shall be included in all - ' copies or substantial portions of the Software. - ' - ' THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR - ' IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, - ' FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE - ' AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER - ' LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, - ' OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE - ' SOFTWARE. - - - - ' /********************************************************************************/ - - ' Summaries: - - - ' Code Statistics: - - ' Total Lines: 168 - ' Code Lines: 142 (84.52%) - ' Comment Lines: 4 (2.38%) - ' - Xml Docs: 0.00% - ' - ' Blank Lines: 22 (13.10%) - ' File Size: 7.01 KB - - - ' Class GCxGCHeatMap - ' - ' Constructor: (+1 Overloads) Sub New - ' - ' Function: GetRectangle - ' - ' Sub: PlotInternal - ' - ' /********************************************************************************/ +' Author: +' +' xieguigang (gg.xie@bionovogene.com, BioNovoGene Co., LTD.) +' +' Copyright (c) 2018 gg.xie@bionovogene.com, BioNovoGene Co., LTD. +' +' +' MIT License +' +' +' Permission is hereby granted, free of charge, to any person obtaining a copy +' of this software and associated documentation files (the "Software"), to deal +' in the Software without restriction, including without limitation the rights +' to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +' copies of the Software, and to permit persons to whom the Software is +' furnished to do so, subject to the following conditions: +' +' The above copyright notice and this permission notice shall be included in all +' copies or substantial portions of the Software. +' +' THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +' IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +' FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +' AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +' LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +' OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +' SOFTWARE. + + + +' /********************************************************************************/ + +' Summaries: + + +' Code Statistics: + +' Total Lines: 168 +' Code Lines: 142 (84.52%) +' Comment Lines: 4 (2.38%) +' - Xml Docs: 0.00% +' +' Blank Lines: 22 (13.10%) +' File Size: 7.01 KB + + +' Class GCxGCHeatMap +' +' Constructor: (+1 Overloads) Sub New +' +' Function: GetRectangle +' +' Sub: PlotInternal +' +' /********************************************************************************/ #End Region Imports System.Drawing -Imports BioNovoGene.Analytical.MassSpectrometry.Assembly.Comprehensive +Imports BioNovoGene.Analytical.MassSpectrometry.GCxGC Imports Microsoft.VisualBasic.ComponentModel.DataSourceModel Imports Microsoft.VisualBasic.ComponentModel.Ranges.Model Imports Microsoft.VisualBasic.Data.ChartPlots.Graphic @@ -99,9 +99,10 @@ Imports GraphicsPath = Microsoft.VisualBasic.Imaging.GraphicsPath Imports FontStyle = Microsoft.VisualBasic.Imaging.FontStyle #End If + Public Class GCxGCHeatMap : Inherits Plot - ReadOnly gcxgc As NamedCollection(Of D2Chromatogram)() + ReadOnly gcxgc As NamedCollection(Of Chromatogram2DScan)() ReadOnly w_rt1 As Double ReadOnly w_rt2 As Double ReadOnly points As NamedValue(Of PointF)() @@ -110,7 +111,7 @@ Public Class GCxGCHeatMap : Inherits Plot Dim dx As Double = 5 Dim dy As Double = 5 - Public Sub New(gcxgc As IEnumerable(Of NamedCollection(Of D2Chromatogram)), + Public Sub New(gcxgc As IEnumerable(Of NamedCollection(Of Chromatogram2DScan)), points As IEnumerable(Of NamedValue(Of PointF)), rt1 As Double, rt2 As Double, @@ -130,13 +131,13 @@ Public Class GCxGCHeatMap : Inherits Plot Me.dy = marginY End Sub - Private Function GetRectangle(gcxgc As D2Chromatogram(), point As PointF) As D2Chromatogram() + Private Function GetRectangle(gcxgc As Chromatogram2DScan(), point As PointF) As Chromatogram2DScan() Dim t1 As New DoubleRange(point.X - w_rt1 / 2, point.X + w_rt1 / 2) Dim t2 As New DoubleRange(point.Y - w_rt2 / 2, point.Y + w_rt2 / 2) Dim scans = gcxgc.Where(Function(i) t1.IsInside(i.scan_time)).OrderBy(Function(i) i.scan_time).ToArray Dim matrix = scans _ .Select(Function(i) - Return New D2Chromatogram With { + Return New Chromatogram2DScan With { .scan_time = i.scan_time, .intensity = i.intensity, .chromatogram = i(t2) @@ -166,14 +167,14 @@ Public Class GCxGCHeatMap : Inherits Plot Dim scaleY As d3js.scale.LinearScale Dim scale As DataScaler Dim n As Double - Dim rowLabelFont As Font = CSS.GetFont(CSSFont.TryParse(theme.axisLabelCSS)) + Dim rowLabelFont As Font = css.GetFont(CSSFont.TryParse(theme.axisLabelCSS)) Dim fontHeight As Double = g.MeasureString("H", rowLabelFont).Height For i As Integer = 0 To matrix.Length - 1 ' for each metabolite row x = rect.Left - For Each col As D2Chromatogram() In matrix(i) + For Each col As Chromatogram2DScan() In matrix(i) scaleX = d3js.scale.linear.domain(values:=col.Select(Function(d) d.scan_time)).range(values:={x, x + wx}) scaleY = d3js.scale.linear.domain(values:=col.Select(Function(d) d.times).IteratesALL).range(values:={y, y + wy}) n = col.Select(Function(d) d.size).Average diff --git a/src/visualize/plot/GCxGC/GCxGCTIC2DPlot.vb b/src/visualize/plot/GCxGC/GCxGCTIC2DPlot.vb index 4021a8b551..5ddf841162 100644 --- a/src/visualize/plot/GCxGC/GCxGCTIC2DPlot.vb +++ b/src/visualize/plot/GCxGC/GCxGCTIC2DPlot.vb @@ -1,65 +1,64 @@ #Region "Microsoft.VisualBasic::a6d9e2fccf734119d1f64dc47798afa0, visualize\plot\GCxGC\GCxGCTIC2DPlot.vb" - ' Author: - ' - ' xieguigang (gg.xie@bionovogene.com, BioNovoGene Co., LTD.) - ' - ' Copyright (c) 2018 gg.xie@bionovogene.com, BioNovoGene Co., LTD. - ' - ' - ' MIT License - ' - ' - ' Permission is hereby granted, free of charge, to any person obtaining a copy - ' of this software and associated documentation files (the "Software"), to deal - ' in the Software without restriction, including without limitation the rights - ' to use, copy, modify, merge, publish, distribute, sublicense, and/or sell - ' copies of the Software, and to permit persons to whom the Software is - ' furnished to do so, subject to the following conditions: - ' - ' The above copyright notice and this permission notice shall be included in all - ' copies or substantial portions of the Software. - ' - ' THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR - ' IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, - ' FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE - ' AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER - ' LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, - ' OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE - ' SOFTWARE. - - - - ' /********************************************************************************/ - - ' Summaries: - - - ' Code Statistics: - - ' Total Lines: 228 - ' Code Lines: 197 (86.40%) - ' Comment Lines: 5 (2.19%) - ' - Xml Docs: 60.00% - ' - ' Blank Lines: 26 (11.40%) - ' File Size: 9.97 KB - - - ' Class GCxGCTIC2DPlot - ' - ' Constructor: (+1 Overloads) Sub New - ' - ' Function: CutSignal, FillHeatMap - ' - ' Sub: FillHeatMap, PlotInternal - ' - ' /********************************************************************************/ +' Author: +' +' xieguigang (gg.xie@bionovogene.com, BioNovoGene Co., LTD.) +' +' Copyright (c) 2018 gg.xie@bionovogene.com, BioNovoGene Co., LTD. +' +' +' MIT License +' +' +' Permission is hereby granted, free of charge, to any person obtaining a copy +' of this software and associated documentation files (the "Software"), to deal +' in the Software without restriction, including without limitation the rights +' to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +' copies of the Software, and to permit persons to whom the Software is +' furnished to do so, subject to the following conditions: +' +' The above copyright notice and this permission notice shall be included in all +' copies or substantial portions of the Software. +' +' THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +' IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +' FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +' AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +' LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +' OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +' SOFTWARE. + + + +' /********************************************************************************/ + +' Summaries: + + +' Code Statistics: + +' Total Lines: 228 +' Code Lines: 197 (86.40%) +' Comment Lines: 5 (2.19%) +' - Xml Docs: 60.00% +' +' Blank Lines: 26 (11.40%) +' File Size: 9.97 KB + + +' Class GCxGCTIC2DPlot +' +' Constructor: (+1 Overloads) Sub New +' +' Function: CutSignal, FillHeatMap +' +' Sub: FillHeatMap, PlotInternal +' +' /********************************************************************************/ #End Region Imports System.Drawing -Imports BioNovoGene.Analytical.MassSpectrometry.Assembly.Comprehensive Imports BioNovoGene.Analytical.MassSpectrometry.Math.Chromatogram Imports Microsoft.VisualBasic.ComponentModel.Ranges.Model Imports Microsoft.VisualBasic.Data.ChartPlots.Graphic @@ -74,6 +73,8 @@ Imports Microsoft.VisualBasic.Math.Distributions Imports Microsoft.VisualBasic.Math.LinearAlgebra Imports Microsoft.VisualBasic.MIME.Html.CSS Imports Microsoft.VisualBasic.MIME.Html.Render +Imports BioNovoGene.Analytical.MassSpectrometry.GCxGC + #If NET48 Then Imports Pen = System.Drawing.Pen @@ -106,25 +107,25 @@ Imports FontStyle = Microsoft.VisualBasic.Imaging.FontStyle ''' Public Class GCxGCTIC2DPlot : Inherits Plot - ReadOnly TIC2D As D2Chromatogram() + ReadOnly TIC2D As Chromatogram2DScan() ReadOnly mapLevels As Integer - Public Sub New(TIC2D As D2Chromatogram(), ql As Double, qh As Double, mapLevels As Integer, theme As Theme) + Public Sub New(TIC2D As Chromatogram2DScan(), ql As Double, qh As Double, mapLevels As Integer, theme As Theme) Call MyBase.New(theme) Me.TIC2D = CutSignal(TIC2D, ql, qh, mapLevels).ToArray Me.mapLevels = mapLevels End Sub - Public Shared Iterator Function CutSignal(gcxgc As D2Chromatogram(), + Public Shared Iterator Function CutSignal(gcxgc As Chromatogram2DScan(), Optional ql As Double = -1, Optional qh As Double = 1, - Optional levels As Integer = 100) As IEnumerable(Of D2Chromatogram) + Optional levels As Integer = 100) As IEnumerable(Of Chromatogram2DScan) If ql <= 0 AndAlso qh >= 1 Then Call "no intensity scale range was changed!".Warning - For Each item As D2Chromatogram In gcxgc + For Each item As Chromatogram2DScan In gcxgc Yield item Next @@ -139,8 +140,8 @@ Public Class GCxGCTIC2DPlot : Inherits Plot Dim qcut As Double = If(qh >= 1, rawData.Max, TrIQ.FindThreshold(rawData, qh, N:=levels)) Dim cutLow As Double = If(ql <= 0, rawData.Min, TrIQ.FindThreshold(rawData, ql, N:=levels)) - For Each scan As D2Chromatogram In gcxgc - Yield New D2Chromatogram With { + For Each scan As Chromatogram2DScan In gcxgc + Yield New Chromatogram2DScan With { .intensity = scan.intensity, .scan_time = scan.scan_time, .chromatogram = scan _ @@ -228,7 +229,7 @@ Public Class GCxGCTIC2DPlot : Inherits Plot ) End Sub - Public Shared Function FillHeatMap(TIC2D As IEnumerable(Of D2Chromatogram), + Public Shared Function FillHeatMap(TIC2D As IEnumerable(Of Chromatogram2DScan), size As Size, scale As DataScaler, Colors As String, @@ -252,7 +253,7 @@ Public Class GCxGCTIC2DPlot : Inherits Plot End Function Public Shared Sub FillHeatMap(g As IGraphics, - TIC2D As IEnumerable(Of D2Chromatogram), + TIC2D As IEnumerable(Of Chromatogram2DScan), dw As Double, dh As Double, scale As DataScaler, @@ -260,7 +261,7 @@ Public Class GCxGCTIC2DPlot : Inherits Plot index As DoubleRange, colors As SolidBrush()) - For Each col As D2Chromatogram In TIC2D + For Each col As Chromatogram2DScan In TIC2D Dim x As Double = scale.TranslateX(col.scan_time) Dim i As Integer Dim rect As RectangleF diff --git a/src/visualize/plot/GCxGC/GCxGCTIC3DPeaks.vb b/src/visualize/plot/GCxGC/GCxGCTIC3DPeaks.vb index 330b5322a3..7d3e85d79b 100644 --- a/src/visualize/plot/GCxGC/GCxGCTIC3DPeaks.vb +++ b/src/visualize/plot/GCxGC/GCxGCTIC3DPeaks.vb @@ -1,65 +1,63 @@ #Region "Microsoft.VisualBasic::08a64e13e93fd879fc5b3aee11a018f0, visualize\plot\GCxGC\GCxGCTIC3DPeaks.vb" - ' Author: - ' - ' xieguigang (gg.xie@bionovogene.com, BioNovoGene Co., LTD.) - ' - ' Copyright (c) 2018 gg.xie@bionovogene.com, BioNovoGene Co., LTD. - ' - ' - ' MIT License - ' - ' - ' Permission is hereby granted, free of charge, to any person obtaining a copy - ' of this software and associated documentation files (the "Software"), to deal - ' in the Software without restriction, including without limitation the rights - ' to use, copy, modify, merge, publish, distribute, sublicense, and/or sell - ' copies of the Software, and to permit persons to whom the Software is - ' furnished to do so, subject to the following conditions: - ' - ' The above copyright notice and this permission notice shall be included in all - ' copies or substantial portions of the Software. - ' - ' THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR - ' IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, - ' FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE - ' AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER - ' LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, - ' OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE - ' SOFTWARE. - - - - ' /********************************************************************************/ - - ' Summaries: - - - ' Code Statistics: - - ' Total Lines: 158 - ' Code Lines: 134 (84.81%) - ' Comment Lines: 6 (3.80%) - ' - Xml Docs: 50.00% - ' - ' Blank Lines: 18 (11.39%) - ' File Size: 7.62 KB - - - ' Class GCxGCTIC3DPeaks - ' - ' Constructor: (+1 Overloads) Sub New - ' - ' Function: MeshGrid - ' - ' Sub: PlotInternal - ' - ' /********************************************************************************/ +' Author: +' +' xieguigang (gg.xie@bionovogene.com, BioNovoGene Co., LTD.) +' +' Copyright (c) 2018 gg.xie@bionovogene.com, BioNovoGene Co., LTD. +' +' +' MIT License +' +' +' Permission is hereby granted, free of charge, to any person obtaining a copy +' of this software and associated documentation files (the "Software"), to deal +' in the Software without restriction, including without limitation the rights +' to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +' copies of the Software, and to permit persons to whom the Software is +' furnished to do so, subject to the following conditions: +' +' The above copyright notice and this permission notice shall be included in all +' copies or substantial portions of the Software. +' +' THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +' IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +' FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +' AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +' LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +' OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +' SOFTWARE. + + + +' /********************************************************************************/ + +' Summaries: + + +' Code Statistics: + +' Total Lines: 158 +' Code Lines: 134 (84.81%) +' Comment Lines: 6 (3.80%) +' - Xml Docs: 50.00% +' +' Blank Lines: 18 (11.39%) +' File Size: 7.62 KB + + +' Class GCxGCTIC3DPeaks +' +' Constructor: (+1 Overloads) Sub New +' +' Function: MeshGrid +' +' Sub: PlotInternal +' +' /********************************************************************************/ #End Region -Imports System.Drawing -Imports BioNovoGene.Analytical.MassSpectrometry.Assembly.Comprehensive Imports BioNovoGene.Analytical.MassSpectrometry.Math.Chromatogram Imports Microsoft.VisualBasic.ComponentModel.Ranges.Model Imports Microsoft.VisualBasic.Data.ChartPlots.Graphic @@ -74,6 +72,8 @@ Imports Microsoft.VisualBasic.Imaging.Drawing3D Imports Microsoft.VisualBasic.Linq Imports Microsoft.VisualBasic.MIME.Html.CSS Imports Microsoft.VisualBasic.MIME.Html.Render +Imports BioNovoGene.Analytical.MassSpectrometry.GCxGC + #If NET48 Then Imports Pen = System.Drawing.Pen @@ -106,11 +106,11 @@ Imports FontStyle = Microsoft.VisualBasic.Imaging.FontStyle ''' Public Class GCxGCTIC3DPeaks : Inherits Plot - ReadOnly raw As D2Chromatogram() + ReadOnly raw As Chromatogram2DScan() ReadOnly sampling As Integer ReadOnly mapLevels As Integer - Public Sub New(gcxgc As D2Chromatogram(), sampling As Integer, mapLevels As Integer, theme As Theme) + Public Sub New(gcxgc As Chromatogram2DScan(), sampling As Integer, mapLevels As Integer, theme As Theme) MyBase.New(theme) Me.raw = gcxgc @@ -171,7 +171,7 @@ Public Class GCxGCTIC3DPeaks : Inherits Plot ) End Sub - Public Shared Iterator Function MeshGrid(gcxgc As D2Chromatogram(), sampling As Integer, xsize As Integer, ysize As Integer, zsize As Integer) As IEnumerable(Of Polygon) + Public Shared Iterator Function MeshGrid(gcxgc As Chromatogram2DScan(), sampling As Integer, xsize As Integer, ysize As Integer, zsize As Integer) As IEnumerable(Of Polygon) Dim height As Integer = gcxgc _ .Select(Function(d) d.size) _ .GroupBy(Function(n) n) _ @@ -185,15 +185,15 @@ Public Class GCxGCTIC3DPeaks : Inherits Plot Dim yscale = d3js.scale.linear.domain(yTicks).range(values:=New Double() {0, ysize}) Dim zscale = d3js.scale.linear.domain(zTicks).range(values:=New Double() {0, zsize}) - gcxgc = (From scan As D2Chromatogram + gcxgc = (From scan As Chromatogram2DScan In gcxgc Where scan.size = height Order By scan.scan_time).ToArray - Dim left As D2Chromatogram = gcxgc(Scan0) + Dim left As Chromatogram2DScan = gcxgc(Scan0) For i As Integer = sampling To gcxgc.Length - 1 Step sampling - Dim right As D2Chromatogram = gcxgc(i) + Dim right As Chromatogram2DScan = gcxgc(i) Dim bottom1 As ChromatogramTick = left(Scan0) Dim bottom2 As ChromatogramTick = right(Scan0) diff --git a/src/visualize/plot/MsPlot.NET5.vbproj b/src/visualize/plot/MsPlot.NET5.vbproj index f5c92d81ad..30495682fa 100644 --- a/src/visualize/plot/MsPlot.NET5.vbproj +++ b/src/visualize/plot/MsPlot.NET5.vbproj @@ -102,10 +102,9 @@ - - + diff --git a/src/visualize/plot/PlotMassWindowXIC.vb b/src/visualize/plot/PlotMassWindowXIC.vb index ebb0c24270..c6729f51a7 100644 --- a/src/visualize/plot/PlotMassWindowXIC.vb +++ b/src/visualize/plot/PlotMassWindowXIC.vb @@ -125,7 +125,7 @@ Public Class PlotMassWindowXIC : Inherits Plot ReadOnly xic As ChromatogramTick() ''' - ''' + ''' Construct a plot that combined of XIC with the scatter density heatmap ''' ''' '''