fix(checks): support 'heavy'/'light' IsotopeLabelType explicitly

R/utils_checks.R

@@ -142,6 +142,24 @@ MSstatsPrepareForDataProcess = function(input, log_base, fix_missing) {
 }
 
 
+#' Map IsotopeLabelType values to canonical "H"/"L" levels
+#' @param x character or factor vector of IsotopeLabelType values
+#' @return factor with levels from \code{c("H","L")} restricted to those present
+#' @keywords internal
+#' @noRd
+.mapIsotopeLabelType = function(x) {
+    label_map <- c(
+        "h"     = "H",
+        "l"     = "L",
+        "heavy" = "H",
+        "light" = "L"
+    )
+    key <- tolower(trimws(as.character(x)))
+    mapped <- unname(label_map[key])
+    factor(mapped, levels = intersect(c("H", "L"), mapped))
+}
+
+
 #' Check validity of data that were not processed by MSstats converter
 #' @param input data.table
 #' @inheritParams MSstatsPrepareForDataProcess
@@ -208,12 +226,7 @@ MSstatsPrepareForDataProcess = function(input, log_base, fix_missing) {
         stop("Statistical tools in MSstats are only proper for label-free or with reference peptide experiments.")
     }
 
-    input$ISOTOPELABELTYPE = factor(input$ISOTOPELABELTYPE)
-    if (data.table::uniqueN(input$ISOTOPELABELTYPE) == 2) {
-        levels(input$ISOTOPELABELTYPE) = c("H", "L")
-    } else {
-        levels(input$ISOTOPELABELTYPE) = "L"
-    }
+    input$ISOTOPELABELTYPE <- .mapIsotopeLabelType(input$ISOTOPELABELTYPE)
     input
 }
 
@@ -231,12 +244,7 @@ MSstatsPrepareForDataProcess = function(input, log_base, fix_missing) {
     }
     input$PEPTIDE = paste(input$PEPTIDESEQUENCE, input$PRECURSORCHARGE, sep = "_")
     input$TRANSITION = paste(input$FRAGMENTION, input$PRODUCTCHARGE, sep = "_")
-    input$ISOTOPELABELTYPE = factor(input$ISOTOPELABELTYPE)
-    if (data.table::uniqueN(input$ISOTOPELABELTYPE) == 2) {
-        levels(input$ISOTOPELABELTYPE) = c("H", "L")
-    } else {
-        levels(input$ISOTOPELABELTYPE) = "L"
-    }
+    input$ISOTOPELABELTYPE <- .mapIsotopeLabelType(input$ISOTOPELABELTYPE)
     input
 }
 

inst/tinytest/test_dataProcess.R

@@ -21,6 +21,14 @@ expect_true(
     "H" %in% QuantDataDefault$FeatureLevelData$LABEL,
     info = "FeatureLevelData should contain heavy-label (H) rows for label-based SRM data"
 )
+expect_true(
+    "L" %in% QuantDataDefault$FeatureLevelData$LABEL,
+    info = "SRMRawData FeatureLevelData must contain L rows"
+)
+expect_true(
+    nrow(QuantDataDefault$ProteinLevelData) > 0,
+    info = "SRMRawData must produce non-empty ProteinLevelData"
+)
 
 
 # Test dataProcess with technical replicates & fractions ------------------

inst/tinytest/test_utils_checks.R

@@ -0,0 +1,92 @@
+# .prepareForDataProcess tests ---------------------------------------------
+input <- data.frame(
+    PeptideModifiedSequence = c("Apeptide", "BPEPTIDE"),
+    PrecursorCharge         = c(2L, 3L),
+    FragmentIon             = c("b2", "y3"),
+    ProductCharge           = c(1L, 1L),
+    IsotopeLabelType        = c("H", "L")
+)
+result_peptideModifiedSequence <- MSstats:::.prepareForDataProcess(input)
+expect_true(
+    "PEPTIDESEQUENCE" %in% colnames(result_peptideModifiedSequence),
+    info = "PEPTIDESEQUENCE should exist after renaming PEPTIDEMODIFIEDSEQUENCE"
+)
+expect_false(
+    "PEPTIDEMODIFIEDSEQUENCE" %in% colnames(result_peptideModifiedSequence),
+    info = "PEPTIDEMODIFIEDSEQUENCE should no longer exist after renaming"
+)
+
+
+make_input <- function(labels) {
+    dt <- data.table::data.table(
+        PeptideSequence = rep("PEPT", length(labels)),
+        PrecursorCharge = rep(2L, length(labels)),
+        FragmentIon     = rep("y3", length(labels)),
+        ProductCharge   = rep(1L, length(labels)),
+        IsotopeLabelType = labels
+    )
+    return(dt)
+}
+
+result <- MSstats:::.prepareForDataProcess(make_input(c("heavy", "light")))
+expect_true(
+    "H" %in% as.character(result$ISOTOPELABELTYPE),
+    info = "label_map: 'heavy' must map to factor level 'H'"
+)
+expect_true(
+    "L" %in% as.character(result$ISOTOPELABELTYPE),
+    info = "label_map: 'light' must map to factor level 'L'"
+)
+expect_equal(
+    levels(result$ISOTOPELABELTYPE), c("H", "L"),
+    info = "label_map: factor levels must be exactly c('H', 'L')"
+)
+
+
+result_light <- MSstats:::.prepareForDataProcess(make_input(rep("light", 4)))
+expect_equal(
+    unique(as.character(result_light$ISOTOPELABELTYPE)), "L",
+    info = "label_map: all 'light' input must produce all 'L' output"
+)
+expect_equal(
+    levels(result_light$ISOTOPELABELTYPE), c("L"),
+    info = "label_map: factor levels for H/L input must still be c('L')"
+)
+
+result_hl <- MSstats:::.prepareForDataProcess(make_input(c("H", "L", "H", "L")))
+expect_equal(
+    as.character(result_hl$ISOTOPELABELTYPE), c("H", "L", "H", "L"),
+    info = "label_map: 'H' / 'L' strings must still pass through unchanged"
+)
+expect_equal(
+    levels(result_hl$ISOTOPELABELTYPE), c("H", "L"),
+    info = "label_map: factor levels for H/L input must still be c('H', 'L')"
+)
+
+result_ll <- MSstats:::.prepareForDataProcess(make_input(rep("L", 5)))
+expect_equal(
+    unique(as.character(result_ll$ISOTOPELABELTYPE)), "L",
+    info = "label_map: all 'L' input must produce all 'L' output"
+)
+
+result_other <- MSstats:::.prepareForDataProcess(make_input(rep("test", 5)))
+expect_true(
+    all(is.na(result_other$ISOTOPELABELTYPE)),
+    info = "Other IsotopeLabelType maps to NA"
+)
+
+result_na <- MSstats:::.prepareForDataProcess(make_input(rep(NA, 5)))
+expect_true(
+    all(is.na(result_na$ISOTOPELABELTYPE)),
+    info = "NA IsotopeLabelType maps to NA"
+)
+
+result_na_l_h <- MSstats:::.prepareForDataProcess(make_input(c(NA, "L", "H")))
+expect_true(
+    any(is.na(result_na_l_h$ISOTOPELABELTYPE)),
+    info = "NA IsotopeLabelType maps to NA"
+)
+expect_equal(
+    levels(result_na_l_h$ISOTOPELABELTYPE), c("H", "L"),
+    info = "label_map: factor levels for H/L input must still be c('H', 'L')"
+)