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tonywu1999tonywu1999
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add unit tests
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‎R/converters_PhilosophertoMSstatsTMTFormat.R‎

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#'
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#' @examples
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#' input_file_path = system.file("tinytest/raw_data/Philosopher/msstats.csv",
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#' package = "MSstatsTMT")
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#' package = "MSstatsConvert")
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#' annotation_file_path = system.file("tinytest/raw_data/Philosopher/MSstatsTMT_annotation.csv",
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#' package = "MSstatsTMT")
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#' package = "MSstatsConvert")
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#' input = data.table::fread(input_file_path)
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#' annotation = data.table::fread(annotation_file_path)
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#' msstats_format = PhilosophertoMSstatsTMTFormat(input, annotation)

‎inst/tinytest/test_converters_MaxQtoMSstatsTMTFormat.R‎

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# Test MaxQtoMSstatsTMTFormat ---------------------------
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mq_ev = data.table::fread(system.file("tinytest/raw_data/MaxQuantTMT/mq_ev.csv",
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package = "MSstatsConvert"))
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mq_pg = data.table::fread(system.file("tinytest/raw_data/MaxQuantTMT/mq_pg.csv",
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package = "MSstatsConvert"))
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annot = data.table::fread(system.file("tinytest/raw_data/MaxQuantTMT/mq_annotation.csv",
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package = "MSstatsConvert"))
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output = MaxQtoMSstatsTMTFormat(mq_ev, mq_pg, annot, use_log_file = FALSE)
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expect_equal(ncol(output), 11)
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expect_true(nrow(output) > 0)
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expect_true("Run" %in% colnames(output))
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expect_true("ProteinName" %in% colnames(output))
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expect_true("PeptideSequence" %in% colnames(output))
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expect_true("Charge" %in% colnames(output))
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expect_true("Intensity" %in% colnames(output))
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expect_true("TechRepMixture" %in% colnames(output))
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expect_true("PSM" %in% colnames(output))
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expect_true("Mixture" %in% colnames(output))
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expect_true("Condition" %in% colnames(output))
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expect_true("BioReplicate" %in% colnames(output))
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expect_true("Channel" %in% colnames(output))
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bad_annotation = data.table::fread(system.file("tinytest/raw_data/PDTMT/pd_annotation.csv",
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package = "MSstatsConvert"))
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expect_error(MaxQtoMSstatsTMTFormat(evidence = mq_ev, proteinGroups = mq_pg,
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annotation = bad_annotation)) # wrong annotation file
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# Verify output intensities are present in input
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intensity_cols = grep("Reporter.intensity.corrected", colnames(mq_ev), value = TRUE)
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input_intensities = as.character(unlist(mq_ev[, intensity_cols, with = FALSE]))
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output_intensities = as.character(output$Intensity[!is.na(output$Intensity)])
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expect_true(all(output_intensities %in% input_intensities))

‎inst/tinytest/test_converters_OpenMStoMSstatsTMTFormat.R‎

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# Test OpenMStoMSstatsTMTFormat ---------------------------
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raw = data.table::fread(system.file("tinytest/raw_data/OpenMSTMT/openmstmt_input.csv",
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package = "MSstatsConvert"))
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output = OpenMStoMSstatsTMTFormat(raw, use_log_file = FALSE)
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expect_equal(ncol(output), 11)
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expect_true(nrow(output) > 0)
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expect_true("Run" %in% colnames(output))
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expect_true("ProteinName" %in% colnames(output))
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expect_true("PeptideSequence" %in% colnames(output))
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expect_true("Charge" %in% colnames(output))
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expect_true("Intensity" %in% colnames(output))
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expect_true("TechRepMixture" %in% colnames(output))
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expect_true("PSM" %in% colnames(output))
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expect_true("Mixture" %in% colnames(output))
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expect_true("Condition" %in% colnames(output))
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expect_true("BioReplicate" %in% colnames(output))
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expect_true("Channel" %in% colnames(output))
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# Verify output intensities are present in input
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input_intensities = as.character(raw$Intensity)
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output_intensities = as.character(output$Intensity[!is.na(output$Intensity)])
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expect_true(all(output_intensities %in% input_intensities))

‎inst/tinytest/test_converters_PDtoMSstatsTMTFormat.R‎

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# Test PDtoMSstatsTMTFormat ---------------------------
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pd_raw = data.table::fread(system.file("tinytest/raw_data/PDTMT/pdtmt_input.csv",
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package = "MSstatsConvert"))
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annot = data.table::fread(system.file("tinytest/raw_data/PDTMT/pd_annotation.csv",
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package = "MSstatsConvert"))
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output = PDtoMSstatsTMTFormat(pd_raw, annot, use_log_file = FALSE)
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expect_equal(ncol(output), 11)
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expect_true(nrow(output) > 0)
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expect_true("Run" %in% colnames(output))
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expect_true("ProteinName" %in% colnames(output))
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expect_true("PeptideSequence" %in% colnames(output))
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expect_true("Charge" %in% colnames(output))
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expect_true("Intensity" %in% colnames(output))
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expect_true("TechRepMixture" %in% colnames(output))
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expect_true("PSM" %in% colnames(output))
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expect_true("Mixture" %in% colnames(output))
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expect_true("Condition" %in% colnames(output))
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expect_true("BioReplicate" %in% colnames(output))
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expect_true("Channel" %in% colnames(output))
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raw.pd = data.table::fread(system.file("tinytest/raw_data/PDTMT/pdtmt_input.csv",
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package = "MSstatsConvert"))
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annotation.pd = data.table::fread(system.file("tinytest/raw_data/PDTMT/pd_annotation.csv",
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package = "MSstatsConvert"))
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expect_error(PDtoMSstatsTMTFormat(input = pd_raw[, !colnames(pd_raw) == "Protein.Accessions"], # missing columns in input
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annotation = annot))
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expect_error(PDtoMSstatsTMTFormat(input = pd_raw,
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annotation = annot[, !colnames(annot) == "Condition"])) # missing columns in annotation
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# Verify output intensities are present in input
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intensity_cols = grep("^Abundance", colnames(pd_raw), value = TRUE)
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input_intensities = as.character(unlist(pd_raw[, intensity_cols, with = FALSE]))
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output_intensities = as.character(output$Intensity[!is.na(output$Intensity)])
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expect_true(all(output_intensities %in% input_intensities))

‎inst/tinytest/test_converters_PhilosophertoMSstatsTMTFormat.R‎

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# Test PhilosophertoMSstatsTMTFormat ---------------------------
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input = data.table::fread(system.file("tinytest/raw_data/Philosopher/msstats.csv",
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package = "MSstatsConvert"))
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annot = data.table::fread(system.file("tinytest/raw_data/Philosopher/MSstatsTMT_annotation.csv",
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package = "MSstatsConvert"))
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output = PhilosophertoMSstatsTMTFormat(input, annot, use_log_file = FALSE)
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expect_equal(ncol(output), 11)
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expect_equal(nrow(output), 550)
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expect_true("Run" %in% colnames(output))
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expect_true("ProteinName" %in% colnames(output))
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expect_true("PeptideSequence" %in% colnames(output))
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expect_true("Charge" %in% colnames(output))
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expect_true("Intensity" %in% colnames(output))
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expect_true("TechRepMixture" %in% colnames(output))
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expect_true("PSM" %in% colnames(output))
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expect_true("Mixture" %in% colnames(output))
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expect_true("Condition" %in% colnames(output))
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expect_true("BioReplicate" %in% colnames(output))
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expect_true("Channel" %in% colnames(output))
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# Verify output intensities are present in input
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intensity_cols = grep("^Channel\\.", colnames(input), value = TRUE)
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input_intensities = as.character(unlist(input[, intensity_cols, with = FALSE]))
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output_intensities = as.character(output$Intensity[!is.na(output$Intensity)])
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expect_true(all(output_intensities %in% input_intensities))

‎inst/tinytest/test_converters_ProteinProspectortoMSstatsTMTFormat.R‎

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# Test ProteinProspectortoMSstatsTMTFormat ---------------------------
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input = system.file("tinytest/raw_data/ProteinProspector/Prospector_TotalTMT.txt",
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package = "MSstatsConvert")
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input = data.table::fread(input)
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annot = system.file("tinytest/raw_data/ProteinProspector/Annotation.csv",
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package = "MSstatsConvert")
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annot = data.table::fread(annot)
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output = ProteinProspectortoMSstatsTMTFormat(input, annot)
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input = data.table::fread(system.file("tinytest/raw_data/ProteinProspector/Prospector_TotalTMT.txt",
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package = "MSstatsConvert"))
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annot = data.table::fread(system.file("tinytest/raw_data/ProteinProspector/Annotation.csv",
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package = "MSstatsConvert"))
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output = ProteinProspectortoMSstatsTMTFormat(input, annot, use_log_file = FALSE)
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expect_equal(ncol(output), 11)
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expect_equal(nrow(output), 528)
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expect_true("Run" %in% colnames(output))
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zero_value_entry =
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output[output$PeptideSequence == "DINKVAEDLESEGLMAEEVQAVQQQEVYGAMPR"
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& output$BioReplicate == "S1",]$Intensity
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expect_true(is.na(zero_value_entry))
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expect_true(is.na(zero_value_entry))
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# Verify output intensities are present in input
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intensity_cols = grep("^Int ", colnames(input), value = TRUE)
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input_intensities = as.character(unlist(input[, intensity_cols, with = FALSE]))
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output_intensities = as.character(output$Intensity[!is.na(output$Intensity)])
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expect_true(all(output_intensities %in% input_intensities))

‎inst/tinytest/test_converters_SpectroMinetoMSstatsTMTFormat.R‎

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# Test SpectroMinetoMSstatsTMTFormat ---------------------------
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raw = data.table::fread(system.file("tinytest/raw_data/SpectroMine/spectromine_input.csv",
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package = "MSstatsConvert"))
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annot = data.table::fread(system.file("tinytest/raw_data/SpectroMine/spectromine_annotation.csv",
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package = "MSstatsConvert"))
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output = SpectroMinetoMSstatsTMTFormat(raw, annot, use_log_file = FALSE)
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expect_equal(ncol(output), 11)
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expect_true(nrow(output) > 0)
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expect_true("Run" %in% colnames(output))
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expect_true("ProteinName" %in% colnames(output))
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expect_true("PeptideSequence" %in% colnames(output))
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expect_true("Charge" %in% colnames(output))
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expect_true("Intensity" %in% colnames(output))
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expect_true("TechRepMixture" %in% colnames(output))
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expect_true("PSM" %in% colnames(output))
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expect_true("Mixture" %in% colnames(output))
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expect_true("Condition" %in% colnames(output))
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expect_true("BioReplicate" %in% colnames(output))
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expect_true("Channel" %in% colnames(output))
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expect_error(SpectroMinetoMSstatsTMTFormat(input = raw,
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annotation = annot,
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summaryforMultipleRows = average)) # wrong argument value
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# Verify output intensities are present in input
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intensity_cols = grep("^PSM\\.TMT", colnames(raw), value = TRUE)
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input_intensities = as.character(unlist(raw[, intensity_cols, with = FALSE]))
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output_intensities = as.character(output$Intensity[!is.na(output$Intensity)])
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expect_true(all(output_intensities %in% input_intensities))
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‎inst/tinytest/test_converters_tmt.R‎

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‎man/PhilosophertoMSstatsTMTFormat.Rd‎

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