MztabParam

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: xcms
-Version: 4.1.7
+Version: 4.1.8
 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,
@@ -97,6 +97,7 @@ Collate:
     'MPI.R'
     'MsExperiment-functions.R'
     'MsExperiment.R'
+    'MzTabParam.R'
     'PlainTextParam.R'
     'RDataParam.R'
     'XcmsExperiment-functions.R'

NAMESPACE

@@ -596,6 +596,7 @@ importFrom("jsonlite", "serializeJSON", "write_json", "unserializeJSON",
            "read_json")
 export("RDataParam")
 export("PlainTextParam")
+export("MzTabParam")
 exportMethods("storeResults")
 
 ## filtering features things

R/AllGenerics.R

@@ -2024,7 +2024,8 @@ setGeneric("stitch.netCDF.new", function(object, lockMass) standardGeneric("stit
 #' - [`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).
+#' - [`MzTabMParam`]: 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.
@@ -2034,7 +2035,7 @@ setGeneric("stitch.netCDF.new", function(object, lockMass) standardGeneric("stit
 #'
 #' @param param The parameter object selecting and configuring the format for
 #' saving. It can be one of the following classes: [`RDataParam`],
-#' [`PlainTextParam`], or `MzTabMParam`.
+#' [`PlainTextParam`], or [`MzTabMParam`].
 #'
 #' @param ... Optional parameters.
 #'
@@ -2059,6 +2060,15 @@ setGeneric("stitch.netCDF.new", function(object, lockMass) standardGeneric("stit
 #' ## Save as a collection of plain text files
 #' storeResults(object = faahko_sub, param = param)
 #'
+#' ## Define param
+#' param <- MzTabParam(studyId = "test",
+#'                     polarity = "positive",
+#'                     sampleDataColumn = "sample_type"
+#'                     path = "test/path/")
+#'
+#' ## Save as a .mzTabm file
+#' storeResults(object = faahko_sub, param = param)
+#'
 #' @md
 setGeneric("storeResults", function(object, param, ...) standardGeneric("storeResults"))
 setGeneric("subset<-", function(object, value) standardGeneric("subset<-"))