R/allGenerics.R

In ethevenot/r-w4m2bioc: Conversion between the Workflow4metabolomics tabulated format and the ExpressionSet bioconductor class

#' Checking the consistency of an ExpressionSet instance with W4M format
#'
#' @param eset An S4 object of class ExpressionSet.
#' @param ... Currently not used.
#' @return Invisible TRUE logical in case of success (otherwise generates an
#' error)
#' @author Etienne Thevenot, \email{etienne.thevenot@@cea.fr}
#' @examples
#' sacSet <- readw4m(file.path(path.package("w4m2bioc"), "extdata"))
#' print(checkw4m(sacSet))
#' @rdname checkw4m
#' @export
setGeneric("checkw4m", function(eset, ...) {standardGeneric("checkw4m")})

#' Exporting ExpressionSet instance into 3 tabulated files.
#'
#' The 3 .tsv files are written with the indicated \code{file} prefix, and
#' '_dataMatrix.tsv', '_sampleMetadata.tsv', and '_variableMetadata.tsv'
#' suffices, respectively. Note that the \code{dataMatrix} is transposed before
#' export (e.g., the samples are written column wise in the 'dataMatrix.tsv'
#' exported file).
#'
#' @param eset An S4 object of class \code{ExpressionSet}
#' function.
#' @param filePrefixC Character: common prefix (including repository full path)
#' of the three file names: for example, the 'c:/mydata/setname' value will
#' result in writting the 'c:/mydata/setname_dataMatrix.tsv',
#' 'c:/mydata/setname_sampleMetadata.tsv', and
#' 'c:/mydata/setname_variableMetadata.tsv' files.
#' @param verboseL Logical: should comments be printed?
#' @param ... Currently not used.
#' @return No object returned.
#' @author Etienne Thevenot, \email{etienne.thevenot@@cea.fr}
#' @examples
#'  sacSet <- readw4m(file.path(path.package("w4m2bioc"), "extdata"))
#'  writew4m(sacSet)
#' @rdname writew4m
#' @export
setGeneric("writew4m", function(eset, ...) standardGeneric("writew4m"))