fix(spectronaut): Enable Fraction column to be processed

Author: tonywu1999

R/clean_Spectronaut.R

@@ -29,8 +29,8 @@
 
   cols = c(protein_col, peptide_col, "FGCharge", "FFrgIon",
            f_charge_col, "RFileName", "RCondition", "RReplicate",
-           "EGQvalue", pg_qval_col, interference_col, exclude_col,
-           intensity_col)
+           "RFraction", "EGQvalue", pg_qval_col, interference_col,
+           exclude_col, intensity_col)
   if (calculateAnomalyScores){
     cols = c(cols, anomalyModelFeatures)
   }
@@ -41,9 +41,10 @@
     spec_input,
     c(protein_col, peptide_col, "FGCharge", "FFrgIon",
       f_charge_col, "RFileName", intensity_col,
-      "RCondition", "RReplicate"),
+      "RCondition", "RReplicate", "RFraction"),
     c("ProteinName", "PeptideSequence", "PrecursorCharge", "FragmentIon",
-      "ProductCharge", "Run", "Intensity", "Condition", "BioReplicate"),
+      "ProductCharge", "Run", "Intensity", "Condition", "BioReplicate",
+      "Fraction"),
     skip_absent = TRUE)
 
   spec_input = .assignSpectronautIsotopeLabelType(

inst/tinytest/test_clean_Spectronaut.R

@@ -9,6 +9,20 @@ output = MSstatsConvert:::.cleanRawSpectronaut(msstats_input, intensity = 'FG.MS
                                     calculateAnomalyScores = FALSE, 
                                     anomalyModelFeatures = c())
 expect_true(all(output$Intensity == 100000))
+# When R.Fraction is absent, no Fraction column is added (prior behavior)
+expect_false("Fraction" %in% colnames(output))
+
+# R.Fraction is transferred and renamed to Fraction when present
+spectronaut_frac = data.table::copy(spectronaut_raw)
+spectronaut_frac$R.Fraction = 2L
+msstats_frac = MSstatsConvert::MSstatsImport(
+    list(input = spectronaut_frac), "MSstats", "Spectronaut")
+output_frac = MSstatsConvert:::.cleanRawSpectronaut(msstats_frac, intensity = 'FG.MS1Quantity',
+                                    calculateAnomalyScores = FALSE,
+                                    anomalyModelFeatures = c())
+expect_true("Fraction" %in% colnames(output_frac))
+expect_false("RFraction" %in% colnames(output_frac))
+expect_true(all(output_frac$Fraction == 2L))
 
 expect_error(MSstatsConvert:::.cleanRawSpectronaut(msstats_input, intensity = 'invalid',
                                                    calculateAnomalyScores = FALSE,