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Output TreeSE #24

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merged 2 commits into from
Mar 14, 2024
+29 −32
Merged

Output TreeSE #24

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TuomasBorman Mar 14, 2024
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TuomasBorman Mar 14, 2024
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@TuomasBorman
TuomasBorman committed Mar 14, 2024
commit 4d1a1b80799d666be70ff313c454bd4aa37725d9
4 changes: 2 additions & 2 deletions tests/testthat/test-getResult.R
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Original file line number Diff line number Diff line change
@@ -15,7 +15,7 @@ test_that("getResult", {
res <- getResult(samples)
# The data must be MAE that have SEs inside
expect_s4_class(res, "MultiAssayExperiment")
expect_s4_class(res[[1]], "SummarizedExperiment")
expect_s4_class(res[[1]], "TreeSummarizedExperiment")

# This function fetches corresponding values from MAE (getResult) and list of
# data.frames (getData)
@@ -95,7 +95,7 @@ test_that("getResult", {
res <- getResult(samples)
# The data must be MAE that have SEs inside
expect_s4_class(res, "MultiAssayExperiment")
expect_s4_class(res[[1]], "SummarizedExperiment")
expect_s4_class(res[[1]], "TreeSummarizedExperiment")

ref <- getMetaboLights(
"https://www.ebi.ac.uk/metabolights/ws/studies/MTBLS4381")

Unchanged files with check annotations Beta

View file
R/getResult.R
rownames(temp) <- accessions
temp <- DataFrame(temp, check.names = FALSE)
# Create empty SE
se <- TreeSummarizedExperiment(colData = temp)

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return(se)
})
names(ses) <- type_names
feat_meta <- DataFrame(feat_meta, check.names = FALSE)
sample_meta <- DataFrame(sample_meta, check.names = FALSE)
# Create TreeSummarizedExperiment
se <- TreeSummarizedExperiment(

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assays = assays, rowData = feat_meta, colData = sample_meta)
# The data still has sample names from MetaboLights and not from HoloFood
# This function cretaes a MAE object from list of tables.
.construct_omics_data_from_markers <- function(res, metadata){
# Convert each table to TreeSummarizedExperiment
res <- lapply(res, .convert_type_to_TreeSummarizedExperiment, metadata)

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# Create MultiAssayExperiment
res <- ExperimentList(res)
res <- MultiAssayExperiment(res)
# Create TreeSummarizedExperiment
assays <- SimpleList(assay)
names(assays) <- assay.type
se <- TreeSummarizedExperiment(

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assays = assays, rowData = row_data,
colData = col_data
)