feat: creation of new generic function so save XcmsExperiment object

R/AllGenerics.R

@@ -1943,6 +1943,51 @@ 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 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.
+#' 
+#' - `PlainTextParam`: Save in a plain text format (to be defined).
+#' 
+#' - `MzTabMParam`: Save in MzTab format (to be defined).
+#' 
+#' For specific examples, see the help pages of the individual parameter classes
+#' listed above.
+#'
+#' @param object 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, Johannes Rainer
+#' 
+#' @example 
+#' 
+#' ## Load a test `XcmsExperiment` object
+#' x <- 
+#' 
+#' Set up parameter to save as .RData file 
+#' param <- RDataParam(fileName = "example_xcms_results")
+#' 
+#' save as .RData
+#' storeResults(object = x, 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/PlainTextParam.R

@@ -0,0 +1,2 @@
+#'
+#'PlainTextParam

R/RDataParam.R

@@ -0,0 +1,70 @@
+#' @title Store `XcmsExperiment` object as .RData file
+#'
+#' @name RDataParam
+#'
+#' @export
+#'
+#' @description
+#' The `RDataParam` class and method allow users to save an `XcmsExperiment`
+#' object as an .RData file with a chosen filename. This new `param` class and
+#' method are part of the possible dispatch of the generic function
+#' `storeResults`. 
+#' 
+#' Other available `param` classes and linked methods include:
+#'
+#' - `PlainTextParam`: ...
+#'
+#' - `MzTabMParam`: ...
+#' 
+#' @param param A parameter defining the format in which the object should be
+#' saved. For the `RDataParam`, it has one slot for the `fileName` in which the
+#' object is going to be saved. The default will be `tempfile()`.
+#'
+#' @param object An object of class `XcmsExperiment` that will be saved as an
+#' .RData file.
+#' 
+#' @return The saved object as an .RData file. 
+#'
+#' @author Philippine Louail
+#'
+#' @examples
+#'
+#'## Get an `XcmsExperiment` object
+#' x <- ...
+#' 
+#' ## Define param 
+#' param <- RDataParam(fileName = "example_xcms_object")
+#' 
+#' ## Save as RData
+#' storeResults(object = x, param = param)
+#' 
+NULL
+
+#' @noRd
+setClass("RDataParam",
+ slots = c(fileName = "character"), 
+ contains = "Param",
+ prototype = prototype(
+ fileName = character()),
+ validity = function(object) {
+ msg <- NULL
+ if (length(object@fileName) != 1) 
+ msg <- c("'fileName' has to be a character string of length 1")
+ msg
+ })
+
+#' @rdname RDataParam
+#'
+#' @export
+RDataParam <- function(fileName = tempfile()) {
+ new("RDataParam", fileName = fileName)
+}
+
+#' @rdname RDataParam
+setMethod("storeResults",
+ signature(object = "XcmsExperiment", 
+ param = "RDataParam"), 
+ function(object, param){
+ save(object, file = param@fileName)
+ }
+ )

tests/testthat.R

@@ -64,6 +64,17 @@ pest_dda <- findChromPeaks(pest_dda, param = cwp)
 ## sciex_data <- readMSData(fl, mode = "onDisk")
 ## sciex_data <- pickPeaks(sciex_data)
 
+library(MsExperiment)
+fls <- normalizePath(faahko_3_files)
+df <- data.frame(mzML_file = basename(fls),
+ dataOrigin = fls,
+ sample = c("ko15", "ko16", "ko18"))
+mse <- readMsExperiment(spectraFiles = fls, sampleData = df)
+p <- CentWaveParam(noise = 10000, snthresh = 40, prefilter = c(3, 10000))
+xmse <- findChromPeaks(mse, param = p)
+pdp <- PeakDensityParam(sampleGroups = rep(1, 3))
+xmseg <- groupChromPeaks(xmse, param = pdp, add = FALSE)
+
 test_check("xcms")
 
 bpstop(prm)

tests/testthat/test_XcmsExperiment.R

@@ -1,14 +1,3 @@
-library(MsExperiment)
-fls <- normalizePath(faahko_3_files)
-df <- data.frame(mzML_file = basename(fls),
- dataOrigin = fls,
- sample = c("ko15", "ko16", "ko18"))
-mse <- readMsExperiment(spectraFiles = fls, sampleData = df)
-p <- CentWaveParam(noise = 10000, snthresh = 40, prefilter = c(3, 10000))
-xmse <- findChromPeaks(mse, param = p)
-pdp <- PeakDensityParam(sampleGroups = rep(1, 3))
-xmseg <- groupChromPeaks(xmse, param = pdp, add = FALSE)
-
 fl <- system.file("TripleTOF-SWATH", "PestMix1_SWATH.mzML", package = "msdata")
 mse_dia <- readMsExperiment(fl)
 
@@ -633,7 +622,7 @@ test_that(".xmse_filter_peaks_intensities works", {
  res <- .xmse_filter_peaks_intensities(xmse, nValues = 1, threshold = 50000)
  expect_equal(res, unname(chromPeaks(xmse)[, "maxo"] >= 50000))
 
- res <- .xmse_filter_peaks_intensities(xmse, nValues = 1, , msLeve = 2L)
+ res <- .xmse_filter_peaks_intensities(xmse, nValues = 1, , msLevel = 2L)
  expect_true(length(res) == 0)
 })
 
@@ -1326,3 +1315,11 @@ test_that("setAs,XcmsExperiment,xcmsSet works", {
  expect_s4_class(res, "xcmsSet")
  expect_equal(peaks(res), chromPeaks(xmseg))
 })
+
+test_that("storeResults,RDataParam works", {
+ param <- RDataParam(fileName ="test")
+ param2 <- RDataParam()
+ expect_false(is.null(param2))
+ storeResults(xmse, param = param)
+ expect_true(file.exists("test"))
+})