Skip to content

Latest commit

 

History

History
507 lines (318 loc) · 14.2 KB

NEWS.md

File metadata and controls

507 lines (318 loc) · 14.2 KB

Spectra 1.11

Changes in 1.11.7

  • Fix in compareSpectra to also pass parameters ppm and tolerance to the peak similarity calculation functions FUN: this allows to use custom similarity function with integrated mapping of peaks.
  • Add joinPeaksNone to skip the peak matching in compareSpectra if the similarity scoring function performs its own peak matching.
  • Only use parallel processing in setBackend,Spectra if both backends support it.

Changes in 1.11.6

  • Add filterPrecursorMaxIntensity function.
  • Add filterPrecursorIsotopes function.

Changes in 1.11.5

Changes in 1.11.4

  • Import uniqueMsLevels from ProtGenerics.

Changes in 1.11.3

  • Rename combinePeaks for lists of peak matrices into combinePeaksData.
  • Add combinePeaks generics.
  • Add combinePeaks,Spectra to combine peaks within each spectrum in a Spectra.

Changes in 1.11.2

  • Add deisotopeSpectra and reduceSpectra functions.

Changes in 1.11.1

  • Add example for filtering precursor m/z peaks from fragment spectra to the vignette.

Spectra 1.9

Changes in 1.9.15

  • Fix issue in MsBackendMemory failed to return intensity or m/z values when peaks data is empty.
  • Fix bug in filterPrecursorScan() (see #194 and PR #277).

Changes in 1.9.14

  • Fix issue with filterMzValues that would only keep (or remove) the first matching peak instead of all matching peaks (given ppm and tolerance). Issue #274.
  • Add parameter keep to filterMzRange to support keeping or removing matching peaks.

Changes in 1.9.13

  • Add the backendBpparam method that allows to evaluate whether a MsBackend supports the provided (or the default) BiocParallel-based parallel processing setup.
  • Minor tweaks in the internal .peaksapply function to avoid splitting/merging of data if not needed (e.g. if no parallel processing is performed).
  • Minor tweaks in spectra comparison functions to avoid repeated calling of functions in loops.

Changes in 1.9.12

  • Extend the list of available MsBackend backends provided by other packages (in the README and in the package vignette).

Changes in 1.9.11

  • Fix headers in MsBackend vignette.

Changes in 1.9.10

  • Add supportsSetBackend method for MsBackend to specify whether a backend supports setBackend,Spectra.
  • setBackend checks using supportsSetBackend whether a backend supports setBackend.

Changes in 1.9.9

  • Refactor setBackend to only split and merge backends if necessary and to not change dataOrigin of the original backend.
  • Support setBackend with MsBackendMemory for an empty Spectra object (issue #268).
  • Disable automatic detection of peak variables for MsBackendMemory (issue #269).
  • Fix issue in Spectra with empty character (issue #267).

Changes in 1.9.8

  • Address comments from Michele Stravs regarding the MsBackend vignette.
  • Add additional tests checking for MsBackend compliance.

Changes in 1.9.7

  • Add a vignette describing how to build a MsBackend from scratch (issue #262).
  • Extend unit test suite to evaluate validity of MsBackend implementations.

Changes in 1.9.6

  • Replace <= with between calls.

Changes in 1.9.5

  • Fix bug in containsMz() when mz isn't ordered (see #258).

Changes in 1.9.4

  • Fix error when extracting spectra variables from a MsBackendMzR of length 0.

Changes in 1.9.3

  • Add chunkapply function to split a Spectra into chunks and stepwise apply a function FUN to each.

Changes in 1.9.2

  • combineSpectra on Spectra with read-only backends change backend to an MsBackendMemory instead of an MsBackendDataFrame.

Changes in 1.9.1

  • Expand documentation on compareSpectra for GNPS-like similarity scoring.

Changes in 1.9.0

  • Bioconductor 3.17 developmental version.

Spectra 1.7

Changes in 1.7.5

  • Force serial processing in some unit tests to avoid potential failures on some Bioconductor build and check servers (under some circumstances).

Changes in 1.7.4

  • Add MsBackendMemory backend class providing a more efficient in-memory data representation than MsBackendDataFrame.

Changes in 1.7.3

  • Import spectrapply from ProtGenerics.

Changes in 1.7.2

  • Fix setBackend if provided Spectra is empty.
  • backendInitialize,Spectra,MsBackendDataFrame returns a Spectra object with the full provided spectra data.

Changes in 1.7.1

  • Add uniqueMsLevels function to allow more efficient, backend-specific, implementations for retrieving unique MS levels from a data set.

Spectra 1.5

Changes in 1.5.20

  • Add parameters ppm and tolerance to PrecursorMzParam (for neutral loss calculation) and add option filterPeaks = "removePrecursor".

Changes in 1.5.19

  • Improved the bin method.

Changes in 1.5.18

  • Set default for parameter columns in peaksData,Spectra and peaksData,MsBackend to c("mz", "intensity").

Changes in 1.5.17

  • Add peaksVariables method and add parameter columns (or ...) to peaksData.
  • Add columns parameter to the peaksData method of MsBackendDataFrame, MsBackendMzR and MsBackendHdf5peaks.

Changes in 1.5.16

  • Fix issue in neutralLoss that would prevent calculation of neutral loss spectra if

Changes in 1.5.15

  • Fix typo in MZ delta plot title.

Changes in 1.5.14

  • Add coreSpectraVariables function to export the core spectra variables and their expected data types.

Changes in 1.5.13

  • Fix figure sizes in vignette.

Changes in 1.5.12

  • Add neutralLoss method and first algorithm to calculate neutral loss spectra.

Changes in 1.5.11

  • Fix neutral loss example in the vignette.

Changes in 1.5.10

  • Add citation.

Changes in 1.5.9

  • Add examples for combineSpectra to the vignette.

Changes in 1.5.8

  • Add spectraVariableMapping generic.

Changes in 1.5.7

  • Add missing export of the filterPrecursorMz method.

Changes in 1.5.6

  • Add filterPrecursorMzValue method which allows to filter using multiple precursor m/z values (issue #230).
  • Fix unit test suite.

Changes in 1.5.5

  • Add a testing framework allowing to run standardized unit tests for new MsBackend implementations (issue #186).

Changes in 1.5.4

  • Add the MsBackendCached backend.

Changes in 1.5.3

  • Only calculate number of peaks per spectra if the processing queue of the Spectra is not empty. Otherwise call the backend's implementation (issue MsBackendSql #31).

Changes in 1.5.2

  • Small documentation update (related to MsCoreUtils issue #87).
  • New countIdentifications() function.
  • Add filterFourierTransformArtefacts function to remove fast fourier artefact peaks seen on e.g. Orbitrap instruments (issue #223).

Changes in 1.5.1

  • Don't read header information when importing peaks matrix on macOS.

Spectra 1.3

Changes in 1.3.11

  • Fix error message in setBackend (issue #217).

Changes in 1.3.10

  • Fix bug in plotSpectra and plotSpectraMirror that would cause an error if the number of peaks in a spectrum was 1 and labels were provided.

Changes in 1.3.9

  • New features: joinSpectraData() now check for duplicated keys in x (throws an error) and y (thows a warning).

Changes in 1.3.8

  • New features: plotMzDelta() function to M/Z delta QC (ported from MSnbase).

Changes in 1.3.7

  • Add fix from MSnbase (issue #170) to Spectra: on macOS require reading also the spectrum header before reading the peaks data.

Changes in 1.3.6

  • Documentation updates for combineSpectra and combinePeaks.

Changes in 1.3.5

  • filterMzValues supports also removing peaks matching specified m/z values (issue #209).

Changes in 1.3.4

  • Add list of additional R packages and repositories providing MsBackend backends to the vignette.

Changes in 1.3.3

  • Move generics for bin and compareSpectra to ProtGenerics.

Changes in 1.3.2

  • Add parameter f to filterPrecursorScan to fix issue #194.

Changes in 1.3.1

  • Add estimatePrecursorIntensity function (issue #202).

Spectra 1.1

Changes in 1.1.20

  • Fix concatenating empty spectra (issue #200).

Changes in 1.1.19

  • New filterPrecursorCharge() method.

Changes in 1.1.18

  • Define plotSpectraMirror as a method.

Changes in 1.1.17

  • Fix issue #187.
  • Add function concatenateSpectra to allow concatenating Spectra objects and list of Spectra objects.

Changes in 1.1.16

  • Support arbitrary spectra variables to be passed to the functions provided/added with addProcessing; issue #182.

Changes in 1.1.15

  • Pass spectras' precursor m/z to the MAPFUN in compareSpectra; issue #171.
  • Add joinPeaksGnps to perform a peak matching between spectra similar to the one performed in GNPS (issue #171).

Changes in 1.1.14

  • Support plotting of empty spectra (issue 175).

Changes in 1.1.13

  • Move ProcessingStep to ProtGenerics.

Changes in 1.1.12

  • Fix show method for Spectra to list only the 3 most recent processing steps (issue 173).
  • Add processingLog function to display the log messages of all processing steps of a Spectra object.

Changes in 1.1.11

  • Add support for ... to pickPeaks and smooth (issue 168).

Changes in 1.1.10

  • Import filterIntensity from ProtGenerics.

Changes in 1.1.9

  • Fix label in plotSpectra.

Changes in 1.1.8

  • filterIntensity supports passing of additional parameters to the used filter function (issue 164).

Changes in 1.1.7

  • Fix bug in show,ProcessingStep (issue 162).

Changes in 1.1.6

  • New joinSpectraData() function.

Changes in 1.1.5

  • Add [[,Msbackend and [[<-,MsBackend methods (issue 149).
  • Add [[,Spectra and [[<-,Spectra methods.

Changes in 1.1.4

  • Fix issue with labelCol in plotSpectra (issue #157).

Changes in 1.1.3

  • Implement a generic Spectra,ANY constructor replacing Spectra,DataFrame and Spectra,character.

Changes in 1.1.2

  • Fix problem in export to mzML files that failed for empty spectra (issue #145)

Changes in 1.1.1

  • Round retention time in figure titles.
  • Document differences between spectrumId (spectrumID), acquisitionNum and scanIndex.

Changes in 1.1.0

  • New Bioc devel version

Spectra 0.99

Changes in 0.99.11

  • Re-add mz and intensity as core spectra variables.

Changes in 0.99.10

  • Fix in spectraData<-,Spectra to avoid removing m/z and intensity values (issue #146).
  • Add default implementations of filter functions for MsBackend.

Changes in 0.99.9

  • Fix in Spectra,character constructor to ensure the backend is changed even if source inherits from backend (issue #143).

Changes in 0.99.8

  • combineSpectra applies data processing steps in the processing queue prior to combination (issue #140).

Changes in 0.99.7

  • Fix problem in dropNaSpectraVariables that would also drop m/z and intensity values for most backends (issue #138.

Changes in 0.99.6

  • Support intensity in filterIntensity method to be a function to enable peak intensity-based filtering of spectra (issue #126).

Changes in 0.99.5

  • Add filterMzRange and filterMzValues to filter spectra based on an m/z range or a list of target m/z values, respectively.

Changes in 0.99.4

  • Add export,MsBackendMzR to export spectra data to mzML or mzXML file(s).
  • Add an export,MsBackend method to allow backends to take care of data export.
  • Refactor export,Spectra to use the MsBackend class to export the data.
  • Change parameter source in Spectra,character to MsBackendMzR and set parameter backend = source. Thus by default, the import backend will also be used to store the data.

Changes in 0.99.3

  • Replace lapply,Spectra with spectrapply,Spectra.

Changes in 0.99.2

  • Replace asDataFrame,MsBackend with spectraData,MsBackend.
  • Replace asDataFrame<-,MsBackend with spectraData<-,MsBackend.
  • Replace as.list,MsBackend with peaksData,MsBackend.
  • Replace replaceList<-,MsBackend with peaksData<-,MsBackend.
  • Replace as.list,Spectra with peaksData,Spectra and add methods to coerce a Spectra to a list or SimpleList.

Changes in 0.99.0

  • Add reset method.
  • Add processing by chunk to compareSpectra.