exportMetaboAnalyst: Export data for use in MetaboAnalyst

Description Usage Arguments Value Author(s)

View source: R/functions-XCMSnExp.R

Description

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

Usage

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

Arguments

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.

Value

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

Author(s)

Johannes Rainer


xcms documentation built on May 18, 2019, 2 a.m.