Merge branch 'devel' into phili

.github/workflows/check-bioc.yml

@@ -124,32 +124,7 @@ jobs:
       - name: Install macOS system dependencies
         if: matrix.config.os == 'macOS-latest'
         run: |
-          ## Enable installing XML from source if needed
-          brew install libxml2
-          echo "XML_CONFIG=/usr/local/opt/libxml2/bin/xml2-config" >> $GITHUB_ENV
-
-          ## Required to install magick as noted at
-          ## https://github.com/r-lib/usethis/commit/f1f1e0d10c1ebc75fd4c18fa7e2de4551fd9978f#diff-9bfee71065492f63457918efcd912cf2
-          brew install imagemagick@6
-
-          ## For textshaping, required by ragg, and required by pkgdown
-          brew install harfbuzz fribidi
-
-          ## For installing usethis's dependency gert
-          brew install libgit2
-
-          ## required for ncdf4
-          ## brew install netcdf ## Does not work as it is compiled with gcc
-          ## Use pre-compiled libraries from https://mac.r-project.org/libs-4/
-          # curl -O https://mac.r-project.org/libs-4/netcdf-4.7.4-darwin.17-x86_64.tar.gz
-          # tar fvxzm netcdf-4.7.4-darwin.17-x86_64.tar.gz -C /
-          # rm netcdf-4.7.4-darwin.17-x86_64.tar.gz
-          # curl -O https://mac.r-project.org/libs-4/hdf5-1.12.0-darwin.17-x86_64.tar.gz
-          # tar fvxzm hdf5-1.12.0-darwin.17-x86_64.tar.gz -C /
-          # rm hdf5-1.12.0-darwin.17-x86_64.tar.gz
-          # curl -O https://mac.r-project.org/libs-4/szip-2.1.1-darwin.17-x86_64.tar.gz
-          # tar fvxzm szip-2.1.1-darwin.17-x86_64.tar.gz -C /
-          # rm szip-2.1.1-darwin.17-x86_64.tar.gz
+        shell: Rscript {0}
 
       - name: Install Windows system dependencies
         if: runner.os == 'Windows'

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: xcms
-Version: 4.3.1
+Version: 4.3.3
 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,
@@ -54,7 +54,7 @@ Imports:
     methods,
     Biobase,
     BiocGenerics,
-    ProtGenerics (>= 1.35.4),
+    ProtGenerics (>= 1.37.1),
     lattice,
     MassSpecWavelet (>= 1.66.0),
     S4Vectors,
@@ -63,9 +63,8 @@ Imports:
     MsCoreUtils (>= 1.15.5),
     MsFeatures,
     MsExperiment (>= 1.5.4),
-    Spectra (>= 1.13.7),
+    Spectra (>= 1.15.7),
     progress,
-    jsonlite,
     RColorBrewer,
     MetaboCoreUtils (>= 1.11.2)
 Suggests:
@@ -93,7 +92,7 @@ URL: https://github.com/sneumann/xcms
 BugReports: https://github.com/sneumann/xcms/issues/new
 VignetteBuilder: knitr
 biocViews: ImmunoOncology, MassSpectrometry, Metabolomics
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Encoding: UTF-8
 Collate:
     'AllGenerics.R'
@@ -104,12 +103,9 @@ Collate:
     'MPI.R'
     'MsExperiment-functions.R'
     'MsExperiment.R'
-    'MzTabParam.R'
-    'XcmsExperiment.R'
-    'PlainTextParam.R'
-    'RDataParam.R'
     'XcmsExperiment-functions.R'
     'XcmsExperiment-plotting.R'
+    'XcmsExperiment.R'
     'c.R'
     'cwTools.R'
     'databases.R'

NAMESPACE

@@ -4,7 +4,8 @@ import("methods")
 importMethodsFrom("ProtGenerics", "peaks", "chromatogram", "writeMSData",
     "polarity<-", "centroided", "isCentroided", "peaks<-",
     "isolationWindowTargetMz", "quantify", "bin", "spectrapply",
-    "filterFeatures", "filterMzRange", "filterRt", "filterMz", "filterMsLevel")
+    "filterFeatures", "filterMzRange", "filterRt", "filterMz", "filterMsLevel",
+    "estimatePrecursorIntensity")
 importClassesFrom("ProtGenerics", "Param")
 importFrom("BiocGenerics", "updateObject", "fileName", "subset",
     "dirname", "dirname<-")
@@ -72,6 +73,7 @@ importMethodsFrom("MSnbase", "intensity", "mz", "rtime", "fileNames", "fromFile"
 importFrom("MSnbase", "as.data.frame.Spectrum", "Chromatogram",
     "MChromatograms", "MSpectra", "requiredFvarLabels", "selectFeatureData")
 
+
 export(
     "etg",
     "medianFilter",
@@ -249,18 +251,19 @@ export(
     "hasFilledChromPeaks",
     "plotAdjustedRtime",
     "groupOverlaps",
-    "estimatePrecursorIntensity",
     "featureArea",
     "loadXcmsData",
     "matchLamasChromPeaks",
     "summarizeLamaMatch",
-    "matchedRtimes"
+    "matchedRtimes",
+    "XcmsExperiment"
 )
 
 ## New analysis methods
 exportMethods(
     "showError",
     "findChromPeaks",
+    "estimatePrecursorIntensity",
     "groupChromPeaks",
     "adjustRtime",
     "findChromPeaksIsolationWindow",
@@ -566,7 +569,8 @@ importMethodsFrom("Spectra", "precursorMz")
 importMethodsFrom("Spectra", "$")
 importMethodsFrom("Spectra", "uniqueMsLevels")
 importMethodsFrom("Spectra", "backendBpparam")
-importFrom("Spectra", "MsBackendMemory")
+importMethodsFrom("Spectra", "estimatePrecursorIntensity")
+importFrom("Spectra", "MsBackendMemory", "filterEmptySpectra")
 
 ## MsExperiment things
 importClassesFrom("MsExperiment", "MsExperiment")
@@ -590,14 +594,6 @@ exportMethods("filterMzRange")
 exportMethods("fromFile")
 exportMethods("fileNames")
 
-## saving xcms objects things
-importFrom("jsonlite", "serializeJSON", "write_json", "unserializeJSON",
-           "read_json")
-export("RDataParam")
-export("PlainTextParam")
-export("MzTabParam")
-exportMethods("storeResults")
-
 ## filtering features things
 importFrom("MetaboCoreUtils", "rowRsd", "rowDratio", "rowPercentMissing",
            "rowBlank", "mclosest")

NEWS.md

@@ -1,5 +1,20 @@
 # xcms 4.3
 
+## Changes in version 4.3.3
+
+- Fix issue #755: `chromatogram()` with `msLevel = 2` fails to extract
+  chromatographic data if `isolationWindowTargetMz` is not specified or
+  available (e.g. for MSe data).
+- Support coercing from `XcmsExperiment` to `XCMSnExp` with
+  `as(object, "XCMSnExp")`.
+- Change `estimatePrecursorIntensity()` to a method and add an implementation
+  for `MsExperiment` objects.
+
+## Changes in version 4.3.2
+
+- Remove data/results import/export functionality as it is being developed in
+  the *MsIO* package.
+
 ## Changes in version 4.3.1
 
 - Support excluding samples or sample groups from defining features with

R/AllGenerics.R

@@ -2050,75 +2050,6 @@ setGeneric("stitch", function(object, lockMass, ...) standardGeneric("stitch"))
 setGeneric("stitch.xml", function(object, lockMass) standardGeneric("stitch.xml"))
 setGeneric("stitch.netCDF", function(object, lockMass) standardGeneric("stitch.netCDF"))
 setGeneric("stitch.netCDF.new", function(object, lockMass) standardGeneric("stitch.netCDF.new"))
-
-#' @title Save xcms result objects in a specified format
-#'
-#' @description
-#'
-#' The `storeResults` function saves an `object` resulting from processing with
-#' the `xcms` package (mainly `XcmsExperiment`). Multiple formats for storing
-#' and exporting are available and can be defined by the `param` argument.
-#'
-#' Supported `param` objects are:
-#'
-#' - [`RDataParam`]: Save in an .RData format file. The name of the file can be
-#'  specified in the `fileName` argument.
-#'
-#' - [`PlainTextParam`]: Store `MsExperiment` and `XcmsExperiment` objects as a
-#' folder of plain text files, folder path defined in the `path` argument.
-#'
-#' - [`MzTabParam`]: Save an `XcmsExperiment` object as a .mztabm format. file
-#' path defined in the `path` argument.
-#'
-#' For specific examples, see the help pages of the individual parameter classes
-#' listed above.
-#'
-#' @param object `MsExperiment` or `XcmsExperiment` The data object that needs
-#' to be saved.
-#'
-#' @param param The parameter object selecting and configuring the format for
-#' saving. It can be one of the following classes: [`RDataParam`],
-#' [`PlainTextParam`], or [`MzTabParam`].
-#'
-#' @param ... Optional parameters.
-#'
-#' @name storeResults
-#'
-#' @author Philippine Louail
-#'
-#' @examples
-#'
-#' ## Load a test data set with detected peaks
-#' library(xcms)
-#' library(MsExperiment)
-#' faahko_sub <- loadXcmsData("faahko_sub2")
-#'
-#' ## Set up parameter to save as .RData file
-#' param <- RDataParam(fileName = "example_xcms_results")
-#'
-#' ## save as .RData
-#' storeResults(object = faahko_sub, param = param)
-#'
-#' ## Set up parameter to save as a collection of plain text file
-#' param <- PlainTextParam(path = "test/path/")
-#'
-#' ## Save as a collection of plain text files
-#' storeResults(object = faahko_sub, param = param)
-#'
-#' ## Get XcmsExperiment object with defined metadata
-#' test_xcms <- loadXcmsData()
-#'
-#' ## Define param
-#' param <- MzTabParam(studyId = "test",
-#'                     polarity = "positive",
-#'                     sampleDataColumn = "sample_type",
-#'                     path = "test/path/")
-#'
-#' ## Save as a .mzTabm file
-#' storeResults(object = test_xcms, param = param)
-#'
-#' @md
-setGeneric("storeResults", function(object, param, ...) standardGeneric("storeResults"))
 setGeneric("subset<-", function(object, value) standardGeneric("subset<-"))
 setGeneric("subsetAdjust", function(object, ...) standardGeneric("subsetAdjust"))
 setGeneric("subsetAdjust<-", function(object, value) standardGeneric("subsetAdjust<-"))

R/MsExperiment-functions.R

@@ -462,7 +462,7 @@
     if (length(msLevel) != npks)
         msLevel <- rep(msLevel[1L], npks)
     if (!length(isolationWindow))
-        isolationWindow <- rep(1L, npks)
+        isolationWindow <- rep(NA_real_, npks)
     if (length(isolationWindow) && length(isolationWindow) != npks)
         stop("Length of 'isolationWindow' (if provided) should match the ",
              "number of chromatograms to extract.")

R/MsExperiment.R

@@ -114,3 +114,16 @@ setMethod(
             msLevel = msLevel, isolationWindow = isolationWindowTargetMz,
             chunkSize = chunkSize, BPPARAM = BPPARAM)
     })
+
+#' @rdname estimatePrecursorIntensity
+setMethod(
+    "estimatePrecursorIntensity", "MsExperiment",
+    function(object, ppm = 10, tolerance = 0,
+             method = c("previous", "interpolation"),
+             BPPARAM = bpparam()) {
+        method <- match.arg(method)
+        estimatePrecursorIntensity(spectra(object), ppm = ppm,
+                                   tolerance = tolerance, method = method,
+                                   f = spectraSampleIndex(object),
+                                   BPPARAM = BPPARAM)
+})