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sneumann / xcms

This is the git repository matching the Bioconductor package xcms: LC/MS and GC/MS Data Analysis
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Suggest for featureValues() #628

Closed DrRuiLi closed 6 days ago

DrRuiLi commented 2 years ago

The default column names in output of featureValues() were fileNames(XCMSnExp) and no other options, should there be other options such as sampleNames(XCMSnExp) or customized vector? image

jorainer commented 2 years ago

Thanks for the suggestion - but I would rather keep it with file names, as sample names are not mandatory and we can not expect that users provide this information at all (or know in which column this information is provided).

Ideally, I would anyway suggest to use the quantify method from xcms that returns a standard Bioconductor SummarizedExperiment object with the feature values as assay data. All additional sample annotations are also provided and stored in the object's colData slot and can in addition be accessed with $. Since the colData needs to have the same order than the columns in assay (or featureValues) it is quite easy to get additional annotations for each column in the feature abundance matrix.