Addition of mzTabParam code

DESCRIPTION

@@ -61,6 +61,7 @@ Collate:
     'MsBackendMzR.R'
     'MsExperiment.R'
     'MsExperimentFiles.R'
+    'MzTabParam.R'
     'Spectra.R'
     'XcmsExperiment.R'
     'zzz.R'

NAMESPACE

@@ -1,6 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
 export(AlabasterParam)
+export(MzTabParam)
 export(PlainTextParam)
 export(readObject)
 exportMethods(readMsObject)

R/MzTabParam.R

@@ -0,0 +1,122 @@
+#' @title Store contents of an `XcmsExperiment` objects as a .mztabm file
+#'
+#' @name MzTabParam
+#'
+#' @export
+#'
+#' @inheritParams saveMsObject
+#'
+#' @family MS object export and import formats.
+#'
+#' @description
+#' The `saveMsObject()` and `readMsObject()` methods with the `MzTabParam`
+#' option enable users to save/load `XcmsExperiment` objects in/from a .mztabm
+#' file format. Mainly the metadata (MTD) and Small molecule feature (SMF)
+#' tables will represent the `XcmsExperiment`. The small molecule summary
+#' section (SML) will be filled with `null` values as no annotation and
+#' identification of compound is performed in `xcms`. Writing data to a folder
+#' that contains already exported data will result in an error.
+#'
+#' @param studyId `character(1)` Will be both the `filename` of the object
+#' saved in .mztabm format and the `mzTab-ID` in the file.
+#'
+#' @param polarity `character(1)` Describes the polarity of the experiment. Two
+#' inputs are possible, "positive" (default) or "negative".
+#'
+#' @param sampleDataColumn `character` strings corresponding to the column
+#' name(s) of the `sampleData()` of the `XcmsExperiment` object with the
+#' different *variables* of the experiment, for example it could be
+#' *"phenotype"*, *"sample_type"*, etc...
+#'
+#' @param path `character(1)` Define where the file is going to be stored. The
+#' default will be `tempdir()`.
+#'
+#' @param optionalFeatureColumns Optional columns from `featureDefinitions`
+#' that should be exported too. For example it could be *"peakidx*,
+#' *"npeaks"*, etc...
+#'
+#' @slot dots `list` Correspond to any optional parameters to be passed
+#' to the `featureValues` function. (e.g. parameters `method` or `value`).
+#'
+#'
+#' @note
+#' This function was build so that the output fit the recommendation of mztab-m
+#' file format. These can be found here:
+#' (http://hupo-psi.github.io/mzTab/2_0-metabolomics-release/mzTab_format_specification_2_0-M_release.html)
+#'
+#' @references
+#'
+#' Hoffmann N, Rein J, Sachsenberg T, Hartler J, Haug K, Mayer G, Alka O,
+#' Dayalan S, Pearce JTM, Rocca-Serra P, Qi D, Eisenacher M, Perez-Riverol Y,
+#' Vizcaino JA, Salek RM, Neumann S, Jones AR. mzTab-M: A Data Standard for
+#' Sharing Quantitative Results in Mass Spectrometry Metabolomics. Anal Chem.
+#' 2019 Mar 5;91(5):3302-3310. doi: 10.1021/acs.analchem.8b04310. Epub 2019 Feb
+#' 13. PMID: 30688441; PMCID: PMC6660005.
+#'
+#' @author Philippine Louail, Johannes Rainer
+#'
+#' @importFrom methods new
+#'
+#' @importClassesFrom ProtGenerics Param
+#'
+#' @examples
+#' ## Load a test data set with detected peaks, of class `XcmsExperiment`
+#' library(xcms)
+#' test_xcms <- loadXcmsData()
+#'
+#' ## Define param
+#' param <- MzTabParam(studyId = "test",
+#'                     polarity = "positive",
+#'                     sampleDataColumn = "sample_type")
+#'
+#' ## Save as a .mzTabm file
+#' saveMsObject(test_xcms, param)
+#'
+NULL
+
+#' @noRd
+setClass("MzTabParam",
+         slots = c(studyId = "character",
+                   polarity = "character",
+                   sampleDataColumn = "character",
+                   path = "character",
+                   optionalFeatureColumns = "character",
+                   dots = "list"
+         ),
+         contains = "Param",
+         prototype = prototype(
+             studyId = character(),
+             polarity =  character(),
+             sampleDataColumn = character(),
+             path = character(),
+             optionalFeatureColumns = character(),
+             dots = list()
+         ),
+         validity = function(object) {
+             msg <- NULL
+             if(length(object@studyId) != 1)
+                 msg <- c("'studyId' has to be a character string of length 1")
+             if(length(object@polarity) != 1)
+                 msg <- c(msg, "'polarity' has to be a character string ",
+                 "of length 1")
+             if(length(object@sampleDataColumn) == 0)
+                 msg <- c(msg, "'sampleDataColumn' cannot be empty")
+             if (length(object@path) != 1)
+                 msg <- c(msg, "'path' has to be a character string of ",
+                 "length 1")
+             msg
+         })
+
+#' @rdname MzTabParam
+#'
+#' @export
+MzTabParam <- function(studyId = character(),
+                       polarity = c("positive", "negative"),
+                       sampleDataColumn = character(),
+                       path = tempdir(),
+                       optionalFeatureColumns = character(), ...) {
+    polarity <- match.arg(polarity)
+    new("MzTabParam", studyId = studyId, polarity = polarity,
+        sampleDataColumn = sampleDataColumn, path = path,
+        optionalFeatureColumns = optionalFeatureColumns, dots = list(...))
+}