inst/tinytest/test_converters_DIAUmpiretoMSstatsFormat.R

In Vitek-Lab/MSstatsConvert: Import Data from Various Mass Spectrometry Signal Processing Tools to MSstats Format

# Test DIAUmpiretoMSstatsFormat ---------------------------

diau_frag = system.file("tinytest/raw_data/DIAUmpire/dia_frag.csv",
                             package = "MSstatsConvert")
diau_pept = system.file("tinytest/raw_data/DIAUmpire/dia_pept.csv",
                             package = "MSstatsConvert")
diau_prot = system.file("tinytest/raw_data/DIAUmpire/dia_prot.csv",
                             package = "MSstatsConvert")
annot = system.file("tinytest/raw_data/DIAUmpire/annot_diau.csv",
                    package = "MSstatsConvert")
diau_frag = data.table::fread(diau_frag)
diau_pept = data.table::fread(diau_pept)
diau_prot = data.table::fread(diau_prot)
annot = data.table::fread(annot)
diau_frag = diau_frag[, lapply(.SD, function(x) if (is.integer(x)) as.numeric(x) else x)]

output = MSstatsConvert:::DIAUmpiretoMSstatsFormat(diau_frag, diau_pept, diau_prot,
                                         annot, use_log_file = FALSE)
expect_equal(ncol(output), 11)
expect_equal(nrow(output), 480)
expect_true("Run" %in% colnames(output))
expect_true("ProteinName" %in% colnames(output))
expect_true("PeptideSequence" %in% colnames(output))
expect_true("PrecursorCharge" %in% colnames(output))
expect_true("Intensity" %in% colnames(output))
expect_true("FragmentIon" %in% colnames(output))
expect_true("ProductCharge" %in% colnames(output))
expect_true("IsotopeLabelType" %in% colnames(output))
expect_true("Condition" %in% colnames(output))
expect_true("BioReplicate" %in% colnames(output))
expect_true("Fraction" %in% colnames(output))