Merge pull request #757 from sneumann/jomain

refactor: dump all data export functionality from xcms

Author: sneumann

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: xcms
-Version: 4.3.1
+Version: 4.3.2
 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,
@@ -65,7 +65,6 @@ Imports:
     MsExperiment (>= 1.5.4),
     Spectra (>= 1.13.7),
     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'
@@ -104,11 +103,9 @@ Collate:
     'MPI.R'
     'MsExperiment-functions.R'
     'MsExperiment.R'
-    'XcmsExperiment.R'
-    'PlainTextParam.R'
-    'RDataParam.R'
     'XcmsExperiment-functions.R'
     'XcmsExperiment-plotting.R'
+    'XcmsExperiment.R'
     'c.R'
     'cwTools.R'
     'databases.R'

NAMESPACE

@@ -72,6 +72,7 @@ importMethodsFrom("MSnbase", "intensity", "mz", "rtime", "fileNames", "fromFile"
 importFrom("MSnbase", "as.data.frame.Spectrum", "Chromatogram",
     "MChromatograms", "MSpectra", "requiredFvarLabels", "selectFeatureData")
 
+
 export(
     "etg",
     "medianFilter",
@@ -254,7 +255,8 @@ export(
     "loadXcmsData",
     "matchLamasChromPeaks",
     "summarizeLamaMatch",
-    "matchedRtimes"
+    "matchedRtimes",
+    "XcmsExperiment"
 )
 
 ## New analysis methods
@@ -566,7 +568,7 @@ importMethodsFrom("Spectra", "precursorMz")
 importMethodsFrom("Spectra", "$")
 importMethodsFrom("Spectra", "uniqueMsLevels")
 importMethodsFrom("Spectra", "backendBpparam")
-importFrom("Spectra", "MsBackendMemory")
+importFrom("Spectra", "MsBackendMemory", "filterEmptySpectra")
 
 ## MsExperiment things
 importClassesFrom("MsExperiment", "MsExperiment")
@@ -590,13 +592,6 @@ exportMethods("filterMzRange")
 exportMethods("fromFile")
 exportMethods("fileNames")
 
-## saving xcms objects things
-importFrom("jsonlite", "serializeJSON", "write_json", "unserializeJSON",
-           "read_json")
-export("RDataParam")
-export("PlainTextParam")
-exportMethods("storeResults")
-
 ## filtering features things
 importFrom("MetaboCoreUtils", "rowRsd", "rowDratio", "rowPercentMissing",
            "rowBlank", "mclosest")

NEWS.md

@@ -1,5 +1,10 @@
 # xcms 4.3
 
+## 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

@@ -2051,61 +2051,6 @@ 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.
-#'
-#' - `MzTabMParam`: Save in MzTab format (to be defined).
-#'
-#' 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 `MzTabMParam`.
-#'
-#' @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)
-#'
-#' @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<-"))