In an previous issue #36 the foldchange function was transferred from stand-alone to public method and split into a metagenomics and omics variant. Replacing the previous DFE public method. But upon closer inspection when dealing with proteomics and transcriptomics data there are several bottlenecks that should be addressed.
Re-factor & generalise function
Address bottlenecks
In an previous issue #36 the
foldchangefunction was transferred from stand-alone to public method and split into ametagenomicsandomicsvariant. Replacing the previousDFEpublic method. But upon closer inspection when dealing withproteomicsandtranscriptomicsdata there are several bottlenecks that should be addressed.Re-factor & generalise function
data.tabletosparseMatrixmethodargument that computes the fold-change of proportional, log-transformed or raw values.Address bottlenecks
feature_mergewhen handling large matrices #40rstatixwith a sparse implementation ofwilcoxtest #42