feat(metamorpheus-converter): Add clean functionality of metamorpheus converter

.gitignore

@@ -5,3 +5,4 @@
 inst/doc
 *.Rproj
 *.DS_Store
+*.log

DESCRIPTION

@@ -29,6 +29,7 @@ Suggests:
     knitr,
     rmarkdown
 Collate: 
+    'clean_Metamorpheus.R'
     'clean_DIANN.R'
     'clean_Philosopher.R'
     'clean_Spectronaut.R'

R/MSstatsConvert_core_functions.R

@@ -271,6 +271,13 @@ setMethod("MSstatsClean", signature = "MSstatsPhilosopherFiles",
 #' @return data.table
 setMethod("MSstatsClean", signature = "MSstatsDIANNFiles", 
           .cleanRawDIANN)
+#' Clean Metamorpheus files
+#' @include clean_Metamorpheus.R
+#' @rdname MSstatsClean
+#' @inheritParams .cleanRawMetamorpheus
+#' @return data.table
+setMethod("MSstatsClean", signature = "MSstatsMetamorpheusFiles", 
+          .cleanRawMetamorpheus)
 
 
 #' Preprocess outputs from MS signal processing tools for analysis with MSstats

R/clean_Metamorpheus.R

@@ -0,0 +1,18 @@
+#' Clean raw Metamorpheus files
+#' @param msstats_object an object of class `MSstatsMetamorpheusFiles`.
+#' @return data.table
+#' @keywords internal
+.cleanRawMetamorpheus = function(msstats_object) {
+    metamorpheus_input = getInputFile(msstats_object, "input")
+    metamorpheus_input = data.table::as.data.table(metamorpheus_input)
+    req_cols = c('FileName', 'ProteinGroup', 'FullSequence', 
+                 'PrecursorCharge', 'Peakintensity')
+    metamorpheus_input = metamorpheus_input[, req_cols, with = FALSE]
+    data.table::setnames(
+        metamorpheus_input, 
+        c("ProteinGroup", "FullSequence", "PrecursorCharge", "FileName", "Peakintensity"),
+        c("ProteinName", "PeptideSequence", "PrecursorCharge", "Run", "Intensity"), 
+        skip_absent = TRUE)
+    .logSuccess("Metamorpheus", "clean")
+    metamorpheus_input
+}

inst/tinytest/raw_data/Metamorpheus/Annotation.tsv

@@ -0,0 +1,5 @@
+Run	Condition	BioReplicate	Fraction
+NEG1-calib	neg	1	1
+NEG2-calib	neg	2	1
+POS1-calib	pos	3	1
+POS2-calib	pos	4	1

inst/tinytest/test_clean_Metamorpheus.R

@@ -0,0 +1,12 @@
+# Test Metamorpheus .cleanRawMetamorpheus ---------------------------
+
+file_path = system.file("tinytest/processed_data/Metamorpheus/MSstatsMetamorpheusFilesObject.rds", package="MSstatsConvert")
+input = readRDS(file_path)
+output = MSstatsConvert:::.cleanRawMetamorpheus(input)
+expect_equal(ncol(output), 5)
+expect_true(nrow(output) > 0)
+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))