feat(Metamorpheus): Remove decoys in converter for Metamorpheus; Add qvalue filtering when MBR is enabled (#108)

Author: tonywu1999

R/clean_Metamorpheus.R

@@ -1,10 +1,28 @@
 #' Clean raw Metamorpheus files
 #' @param msstats_object an object of class `MSstatsMetamorpheusFiles`.
+#' @param MBR If TRUE, the function will include peaks detected by MBR
+#' @param qvalue_cutoff The q-value cutoff for filtering peaks detected by MBR
 #' @return data.table
 #' @keywords internal
-.cleanRawMetamorpheus = function(msstats_object) {
+.cleanRawMetamorpheus = function(msstats_object, MBR = TRUE, qvalue_cutoff = 0.05) {
     metamorpheus_input = getInputFile(msstats_object, "input")
     metamorpheus_input = data.table::as.data.table(metamorpheus_input)
+    # Remove peptide decoys 
+    if ("DecoyPeptide" %in% colnames(metamorpheus_input)) {
+        metamorpheus_input <- metamorpheus_input[!metamorpheus_input$DecoyPeptide, ]
+    }
+    # Remove peak decoys
+    if ("RandomRT" %in% colnames(metamorpheus_input)) {
+        metamorpheus_input <- metamorpheus_input[!metamorpheus_input$RandomRT, ]
+    }
+    if (MBR) {
+        metamorpheus_input = metamorpheus_input[
+            metamorpheus_input$PeakDetectionType == "MSMS" | 
+                metamorpheus_input$`PIPQ-Value` <= qvalue_cutoff , ]
+    } else {
+        metamorpheus_input = metamorpheus_input[
+            metamorpheus_input$PeakDetectionType == "MSMS", ]
+    }
     req_cols = c('FileName', 'ProteinGroup', 'FullSequence', 
                  'PrecursorCharge', 'Peakintensity')
     metamorpheus_input = metamorpheus_input[, req_cols, with = FALSE]

R/converters_MetamorpheusToMSstatsFormat.R

@@ -1,7 +1,9 @@
 #' Import Metamorpheus files
 #' 
 #' @param input name of Metamorpheus output file, which is tabular format. Use the AllQuantifiedPeaks.tsv file from the Metamorpheus output.
-#' @param annotation name of 'annotation.txt' data which includes Condition, BioReplicate. 
+#' @param annotation name of 'annotation.txt' data which includes Condition, BioReplicate.
+#' @param MBR If TRUE, the function will include peaks detected by MBR
+#' @param qvalue_cutoff The q-value cutoff for filtering peaks detected by MBR 
 #' @inheritParams .sharedParametersAmongConverters
 #' 
 #' @return data.frame in the MSstats required format.
@@ -11,17 +13,18 @@
 #' @export
 #' 
 #' @examples 
-#' input = system.file("tinytest/raw_data/Metamorpheus/AllQuantifiedPeaks.tsv", 
+#' input = system.file("tinytest/raw_data/Metamorpheus/QuantifiedPeaks.tsv", 
 #'                                 package = "MSstatsConvert")
 #' input = data.table::fread(input)
-#' annot = system.file("tinytest/raw_data/Metamorpheus/Annotation.tsv", 
+#' annot = system.file("tinytest/raw_data/Metamorpheus/annotation.csv", 
 #'                                 package = "MSstatsConvert")
 #' annot = data.table::fread(annot)
 #' metamorpheus_imported = MSstatsConvert:::MetamorpheusToMSstatsFormat(input, annotation = annot)
 #' head(metamorpheus_imported)
 #' 
 MetamorpheusToMSstatsFormat = function(
-        input, annotation = NULL, useUniquePeptide = TRUE, removeFewMeasurements = TRUE,
+        input, annotation = NULL, MBR = TRUE, qvalue_cutoff = 0.05, 
+        useUniquePeptide = TRUE, removeFewMeasurements = TRUE,
         removeProtein_with1Feature = FALSE, summaryforMultipleRows = max,
         use_log_file = TRUE, append = FALSE, verbose = TRUE, log_file_path = NULL,
         ...
@@ -31,7 +34,7 @@ MetamorpheusToMSstatsFormat = function(
 
     input = MSstatsConvert::MSstatsImport(list(input = input), 
                                           "MSstats", "Metamorpheus", ...)
-    input = MSstatsConvert::MSstatsClean(input)
+    input = MSstatsConvert::MSstatsClean(input, MBR, qvalue_cutoff)
     annotation = MSstatsConvert::MSstatsMakeAnnotation(input, annotation)
 
     feature_columns = c("PeptideSequence", "PrecursorCharge")

inst/tinytest/processed_data/Metamorpheus/MSstatsMetamorpheusFilesObject.rds

@@ -0,0 +1,5 @@
+"Run","BioReplicate","Condition"
+"B03_05_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib",5,"E"
+"B03_06_150304_human_ecoli_E_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib",6,"E"
+"B03_10_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib",10,"A"
+"B03_11_150304_human_ecoli_A_3ul_3um_column_95_HCD_OT_2hrs_30B_9B-calib",11,"A"

inst/tinytest/raw_data/Metamorpheus/AllQuantifiedPeaks.tsv

@@ -211,6 +211,6 @@ expect_true(nrow(sn_cleaned) > 0)
 expect_equal(sn_cleaned, sn_cleaned2)
 
 # Metamorpheus
-metamorpheus_table = data.table::fread("./raw_data/Metamorpheus/AllQuantifiedPeaks.tsv")
+metamorpheus_table = data.table::fread("./raw_data/Metamorpheus/QuantifiedPeaks.tsv")
 input = MSstatsConvert::MSstatsImport(list(input = metamorpheus_table), "MSstats", "Metamorpheus")
 expect_identical(is(input), c("MSstatsMetamorpheusFiles", "MSstatsInputFiles"))

inst/tinytest/raw_data/Metamorpheus/Annotation.tsv

@@ -1,12 +1,12 @@
 # Test MetamorpheusToMSstatsFormat ---------------------------
 
-input_file_path = system.file("tinytest/raw_data/Metamorpheus/AllQuantifiedPeaks.tsv", package="MSstatsConvert")
-annotation_file_path = system.file("tinytest/raw_data/Metamorpheus/Annotation.tsv", package = "MSstatsConvert")
+input_file_path = system.file("tinytest/raw_data/Metamorpheus/QuantifiedPeaks.tsv", package="MSstatsConvert")
+annotation_file_path = system.file("tinytest/raw_data/Metamorpheus/annotation.csv", package = "MSstatsConvert")
 input = data.table::fread(input_file_path)
 annotation = data.table::fread(annotation_file_path)
 output = MSstatsConvert:::MetamorpheusToMSstatsFormat(input, annotation = annotation)
 expect_equal(ncol(output), 11)
-expect_equal(nrow(output), 236)
+expect_equal(nrow(output), 20)
 expect_true("Run" %in% colnames(output))
 expect_true("ProteinName" %in% colnames(output))
 expect_true("PeptideSequence" %in% colnames(output))