fix: ensure MS level is of type integer in Chromatogram

- Ensure MS levels are converted to integer when Chromatogram is extracted from
  a `MsExperiment` or `XcmsExperiment`.

.github/workflows/check-bioc.yml

@@ -52,7 +52,7 @@ jobs:
  fail-fast: false
  matrix:
  config:
- - { os: ubuntu-latest, r: 'devel', bioc: 'devel', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
+ - { os: ubuntu-latest, r: '4.3', bioc: '3.18', cont: "bioconductor/bioconductor_docker:RELEASE_3_18", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
  - { os: macOS-latest, r: '4.3', bioc: '3.18'}
  - { os: windows-latest, r: '4.3', bioc: '3.18'}
  env:

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: xcms
-Version: 4.0.0
+Version: 4.0.1
 Title: LC-MS and GC-MS Data Analysis
 Description: Framework for processing and visualization of chromatographically
  separated and single-spectra mass spectral data. Imports from AIA/ANDI NetCDF,

R/XcmsExperiment.R

@@ -839,7 +839,7 @@ 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,
@@ -1535,7 +1535,7 @@ 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)))))
@@ -1821,7 +1821,7 @@ 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)

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

@@ -1,3 +1,10 @@
+Changes in version 4.0.1
+----------------------
+
+- Ensure MS levels are always provided as integer to `Chromatogram` objects when
+ extracted from `XcmsExperiment` or `MsExperiment`.
+
+
 Changes in version 3.99.6
 ----------------------
 

tests/testthat/test_XcmsExperiment.R

@@ -69,6 +69,7 @@ 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)
@@ -84,13 +85,16 @@ 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))