fix: ensure ms_level column in chromPeaksData is integer

- Ensure the "ms_level" column in the `chromPeaksData` is of type `integer` to
  avoid obscure validity errors on extracted `Chromatogram` objects (happening
  randomly).

R/XcmsExperiment.R

@@ -858,7 +858,7 @@ setMethod(
  chunkSize = chunkSize, BPPARAM = BPPARAM)
  }
  ## Assign/define peak IDs.
- pkd <- data.frame(ms_level = rep(msLevel, nrow(res)),
+ pkd <- data.frame(ms_level = rep(as.integer(msLevel), nrow(res)),
  is_filled = rep(FALSE, nrow(res)))
  ph <- XProcessHistory(param = param,
  type. = .PROCSTEP.PEAK.DETECTION,
@@ -1224,7 +1224,7 @@ setMethod(
  maxi <- max(
  0, as.integer(sub("CP", "", rownames(chromPeaks(object)))))
  rownames(res) <- .featureIDs(nr, "CP", maxi + 1)
- pkd <- data.frame(ms_level = rep(msLevel, nr),
+ pkd <- data.frame(ms_level = rep(as.integer(msLevel), nr),
  is_filled = rep(FALSE, nr))
  rownames(pkd) <- rownames(res)
  pb$tick()
@@ -1554,7 +1554,7 @@ setMethod(
  stop("No chromatographic peaks present. ",
  "Please run 'findChromPeaks' first.")
  res <- .manual_feature_definitions(chromPeaks(object), peakIdx)
- res$ms_level <- msLevel
+ res$ms_level <- as.integer(msLevel)
  if (hasFeatures(object)) {
  maxi <- max(as.integer(
  sub("FT", "", rownames(featureDefinitions(object)))))
@@ -1840,7 +1840,7 @@ setMethod(
  nr <- nrow(res)
  maxi <- max(as.integer(sub("CP", "", rownames(chromPeaks(object)))))
  rownames(res) <- .featureIDs(nr, "CP", maxi + 1)
- cpd <- data.frame(ms_level = rep(msLevel, nr),
+ cpd <- data.frame(ms_level = rep(as.integer(msLevel), nr),
  is_filled = rep(TRUE, nr))
  rownames(cpd) <- rownames(res)
  object@chromPeaks <- rbind(object@chromPeaks, res)
@@ -1976,6 +1976,3 @@ setMethod(
  object[i = sort(unique(file)), keepAdjustedRtime = keepAdjustedRtime,
  keepFeatures = keepFeatures, ...]
  })
-
-## TODO filterMsLevel? Function not yet needed. In case, needs also an
-## implementation for MsExperiment: update the spectra-sample-mapping.

R/functions-utils.R

@@ -816,6 +816,7 @@ groupOverlaps <- function(xmin, xmax) {
  pks_tmz = rep(1L, nrow(pks)),
  aggregationFun = "sum") {
  nr <- nrow(pks)
+ pks_msl <- as.integer(pks_msl)
  FUN <- switch(aggregationFun,
  "sum" = getFunction("sumi"),
  "max" = getFunction("maxi"),

inst/NEWS

@@ -1,6 +1,8 @@
 Changes in version 4.1.4
 ----------------------
 
+- Fix errors related to invalid `Chromatogram` objects extracted from xcms
+ results: ensure MS level in `chromPeaksMatrix` is `integer`.
 - Fix definition of anchor peaks for peakGroups alignment with subset
  (issue #702).
 - Add `filterMsLevel` method for `MsExperiment` and `XcmsExperiment`.

tests/testthat/test_Chromatogram.R

@@ -1,5 +1,5 @@
 ## test_that("extractChromatograms is deprecated", {
-  skip_on_os(os = "windows", arch = "i386")
+## skip_on_os(os = "windows", arch = "i386")
 
 ## expect_warning(chrs <- extractChromatograms(
 ## filterRt(filterFile(od_x, file = 2), c(2500, 2600))))

tests/testthat/test_XcmsExperiment.R

@@ -58,6 +58,7 @@ test_that("findChromPeaks,MsExperiment et al works", {
  expect_true(is.data.frame(chromPeakData(xmse, return.type = "data.frame")))
  expect_s4_class(chromPeakData(xmse), "DataFrame")
  expect_true(nrow(chromPeakData(xmse, 2:3)) == 0)
+ expect_true(is.integer(chromPeakData(res)$ms_level))
 
  ## dropChromPeaks
  rres <- dropChromPeaks(res)
@@ -73,13 +74,16 @@ test_that("findChromPeaks,MsExperiment et al works", {
  expect_equal(res@chromPeaks, res2@chromPeaks)
  expect_equal(res@chromPeakData, res2@chromPeakData)
  expect_true(length(res2@processHistory) == 2)
+ expect_true(is.integer(chromPeakData(res2)$ms_level))
 
  res2 <- findChromPeaks(res, param = p, msLevel = 2L, add = FALSE)
  expect_equal(nrow(res2@chromPeaks), 0)
  expect_true(length(res2@processHistory) == 1)
+ expect_true(is.integer(chromPeakData(res2)$ms_level))
 
  res2 <- findChromPeaks(mse, param = p, chunkSize = -1)
  expect_equal(res@chromPeaks, res2@chromPeaks)
+ expect_true(is.integer(chromPeakData(res2)$ms_level))
 
  expect_true(hasChromPeaks(res))
  expect_true(hasChromPeaks(res, msLevel = 1L))