feat: add filterMsLevel method for MsExperiment and XcmsExperiment

- Add the `filterMsLevel` methods for `MsExperiment` and `XcmsExperiment`.

R/MsExperiment.R

@@ -20,6 +20,14 @@ setMethod("filterMz", "MsExperiment",
  filterMzRange(object, mz, msLevel.)
  })
 
+#' @rdname XcmsExperiment
+setMethod("filterMsLevel", "MsExperiment",
+ function(object, msLevel. = uniqueMsLevels(object)) {
+ message("Filter spectra")
+ .mse_filter_spectra(object, filterMsLevel,
+ msLevel. = msLevel.)
+ })
+
 #' @rdname XcmsExperiment
 setMethod("uniqueMsLevels", "MsExperiment", function(object) {
  uniqueMsLevels(spectra(object))

R/XcmsExperiment.R

@@ -83,6 +83,9 @@
 #' `"isolationWindowUpperMz"` (columns in `chromPeakData`) do not contain
 #' the user provided `mz`.
 #'
+#' - `filterMsLevel`: filter the data of the `XcmsExperiment` or `MsExperiment`
+#' to keep only data of the MS level(s) specified with parameter `msLevel.`.
+#'
 #' - `filterMz`, `filterMzRange`: filter the spectra within an
 #' `XcmsExperiment` or `MsExperiment` to the specified m/z range (parameter
 #' `mz`). For `XcmsExperiment` also identified chromatographic peaks and
@@ -482,6 +485,8 @@
 #' length equal to the numer of rows of the parameters `mz` and `rt`
 #' defining the m/z and rt regions from which the chromatograms should
 #' be created. Defaults to `msLevel = 1L`.
+#' for `filterMsLevel`: `integer` defining the MS level(s) to which the
+#' data should be subset.
 #'
 #' @param mz For `chromPeaks` and `featureDefinitions`: `numeric(2)` optionally
 #' defining the m/z range for which chromatographic peaks or feature
@@ -816,6 +821,20 @@ setMethod(
  callNextMethod(object = object, mz = mz, msLevel. = msLevel.)
  })
 
+#' @rdname XcmsExperiment
+setMethod(
+ "filterMsLevel", "XcmsExperiment",
+ function(object, msLevel. = uniqueMsLevels(object)) {
+ if (!length(msLevel.))
+ return(object)
+ if (hasChromPeaks(object)) {
+ keep <- chromPeakData(object)$ms_level %in% msLevel.
+ object <- .filter_chrom_peaks(object, idx = base::which(keep))
+ }
+ callNextMethod(object = object, msLevel. = msLevel.)
+ })
+
+
 ################################################################################
 ## chromatographic peaks
 ################################################################################

R/methods-XCMSnExp.R

@@ -1460,6 +1460,8 @@ setMethod("smooth", "XCMSnExp", function(x, method = c("SavitzkyGolay",
 setAs(from = "XCMSnExp", to = "xcmsSet", def = .XCMSnExp2xcmsSet)
 
 #' @rdname XcmsExperiment
+#'
+#' @name XcmsExperiment
 setAs(from = "XcmsExperiment", to = "xcmsSet", def = .XCMSnExp2xcmsSet)
 
 #' @rdname XCMSnExp-peak-grouping-results

inst/NEWS

@@ -1,3 +1,10 @@
+Changes in version 4.1.x
+----------------------
+
+- Add `filterMsLevel` method for `MsExperiment` and `XcmsExperiment`.
+- Ensure chunk-wise processing of Spectra (introduced with version 1.13.2) is
+ disabled when xcms is using its own chunk-wise processing.
+
 Changes in version 4.1.1
 ----------------------
 

tests/testthat/test_MsExperiment.R

@@ -16,6 +16,18 @@ test_that("filterRt,MsExperiment works", {
  expect_equal(rtime(spectra(res)), rtime(spectra(mse)))
 })
 
+test_that("filterMsLevel,MsExperiment works", {
+ res <- filterMsLevel(mse, msLevel = 1)
+ expect_equal(rtime(res), rtime(mse))
+
+ res <- filterMsLevel(mse, msLevel = integer())
+ expect_equal(rtime(res), rtime(mse))
+
+ res <- filterMsLevel(mse, msLevel = 2L)
+ expect_equal(rtime(res), numeric())
+ expect_equal(length(res), 3L)
+})
+
 test_that("filterFile,MsExperiment works", {
  res <- filterFile(mse)
  expect_s4_class(res, "MsExperiment")

tests/testthat/test_XcmsExperiment.R

@@ -194,6 +194,16 @@ test_that("filterRt,XcmsExperiment works", {
  seq_len(nrow(chromPeaks(res))))
 })
 
+test_that("filterMsLevel,XcmsExperiment works", {
+ res <- filterMsLevel(xmse, c(1L, 2L))
+ expect_equal(rtime(res), rtime(xmse))
+ expect_equal(chromPeaks(res), chromPeaks(xmse))
+
+ res <- filterMsLevel(xmse, msLevel = 2L)
+ expect_equal(rtime(res), numeric())
+ expect_true(nrow(chromPeaks(res)) == 0L)
+})
+
 test_that("filterFile,XcmsExperiment works", {
  res <- filterFile(xmse)
  expect_s4_class(res, "XcmsExperiment")