Export data for use in MetaboAnalyst — exportMetaboAnalyst • xcms

Export the feature table for further analysis in the MetaboAnalyst software (or the MetaboAnalystR R package).

Usage

exportMetaboAnalyst(
  x,
  file = NULL,
  label,
  value = "into",
  digits = NULL,
  groupnames = FALSE,
  ...
)

x: XCMSnExp object with identified chromatographic peaks grouped across samples.
file: character(1) defining the file name. If not specified, the matrix with the content is returned.
label: either character(1) specifying the phenodata column in x defining the sample grouping or a vector with the same length than samples in x defining the group assignment of the samples.
value: character(1) specifying the value to be returned for each feature. See featureValues() for more details.
digits: integer(1) defining the number of significant digits to be used for numeric. The default NULL uses getOption("digits"). See format() for more information.
groupnames: logical(1) whether row names of the resulting matrix should be the feature IDs (groupnames = FALSE; default) or IDs that are composed of the m/z and retention time of the features (in the format M<m/z>T<rt> (groupnames = TRUE). See help of the groupnames function for details.
...: additional parameters to be passed to the featureValues() function.

If file is not specified, the function returns the matrix in the format supported by MetaboAnalyst.

Johannes Rainer