# Test ProteinProspectortoMSstatsTMTFormat ---------------------------
input = system.file("tinytest/raw_data/ProteinProspector/Prospector_TotalTMT.txt",
package = "MSstatsConvert")
input = data.table::fread(input)
annot = system.file("tinytest/raw_data/ProteinProspector/Annotation.csv",
package = "MSstatsConvert")
annot = data.table::fread(annot)
output = ProteinProspectortoMSstatsTMTFormat(input, annot)
expect_equal(ncol(output), 11)
expect_equal(nrow(output), 528)
expect_true("Run" %in% colnames(output))
expect_true("ProteinName" %in% colnames(output))
expect_true("PeptideSequence" %in% colnames(output))
expect_true("Charge" %in% colnames(output))
expect_true("Intensity" %in% colnames(output))
expect_true("TechRepMixture" %in% colnames(output))
expect_true("PSM" %in% colnames(output))
expect_true("Mixture" %in% colnames(output))
expect_true("Condition" %in% colnames(output))
expect_true("BioReplicate" %in% colnames(output))
expect_true("Channel" %in% colnames(output))
# Test ProteinProspectortoMSstatsTMTFormat with missing value ------------
zero_value_entry =
output[output$PeptideSequence == "DINKVAEDLESEGLMAEEVQAVQQQEVYGAMPR"
& output$BioReplicate == "S1",]$Intensity
expect_true(is.na(zero_value_entry))
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