metWrite: Exporting a MultiDataSet instance into dataset subfolders,...
In ethevenot/metabolis: Metabolomics Data Analysis

Description Usage Arguments Value Author(s) Examples

Note that the dataMatrix is transposed before export (e.g., the samples are written column wise in the 'dataMatrix.tsv' exported file).

metWrite(x, ...)

## S4 method for signature 'MultiDataSet'
metWrite(x, dirC, filesLs = NULL,
  overwriteL = FALSE, info.txtC = NA)

## S4 method for signature 'ExpressionSet'
metWrite(x, dirC, dataMatrix.tsvC = NA,
  sampleMetadata.tsvC = NA, variableMetadata.tsvC = NA,
  overwriteL = FALSE, info.txtC = NA)

`x`	An S4 object of class `MultiDataSet`
`dirC`	Character: directory where each dataset subfolder should be created
`overwriteL`	Logical: should existing files be overwritten?
`info.txtC`	Character: File name for the printed results (call to 'sink()'); if NA (default), messages will be printed on the screen; if NULL, no verbose will be generated
`dataMatrix.tsvC`	Character: alternatively, the FULL name of the dataMatrix, sampleMetadata, and variableMetadata files can be specified here and in the following two arguments (in that case, the dirC argument must be set to NA); note that if the sampleMetadata and/or variableMetadata file names are left to NA, the corresponding phenoData and featureData slots will be empty in the output ExpressionSet.
`sampleMetadata.tsvC`	Character: full name of the sampleMetadata file (when dirC is set to NA)
`variableMetadata.tsvC`	Character: full name of the variableMetadata file (when dirC is set to NA)
`fileLs`	List: alternatively to the dirC argument, the full names of the files can be provided as a list
`x`	An S4 object of class `ExpressionSet`
`dirC`	Character: directory where each dataset should be written
`overwriteL`	Logical: should existing files be overwritten?
`info.txtC`	Character: File name for the printed results (call to 'sink()'); if NA (default), messages will be printed on the screen; if NULL, no verbose will be generated

No object returned.

Etienne Thevenot, etienne.thevenot@cea.fr

prometMset <- metRead(system.file("extdata/promet",package="metabolis"))
## Not run: 
metWrite(prometMset, dirC = file.path(getwd(), "promet"))
# alternatively
metWrite(prometMset,
         dirC = NA,
         filesLs = list(metabo = list(dataMatrix.tsvC = file.path(getwd(), "met_dataMatrix.tsv"),
                                      sampleMetadata.tsvC = file.path(getwd(), "met_sampleMetadata.tsv"),
                                      variableMetadata.tsvC = file.path(getwd(), "met_variableMetadata.tsv")),
                        proteo = list(dataMatrix.tsvC = file.path(getwd(), "pro_dataMatrix.tsv"),
                                      sampleMetadata.tsvC = file.path(getwd(), "pro_sampleMetadata.tsv"),
                                      variableMetadata.tsvC = file.path(getwd(), "pro_variableMetadata.tsv"))))

## End(Not run)

metSet <- metabolis::metRead(system.file("extdata/promet/metabo", package="metabolis"))
## Not run: 
metWrite(metSet, dirC = file.path(getwd(), "metabo"))

## End(Not run)