def runDESeq( infiles, outfile ): '''estimate differential expression using DESeq. The final output is a table. It is slightly edited such that it contains a similar output and similar fdr compared to cuffdiff. ''' PipelineWindows.runDE( infiles, outfile, "deseq.dir", method = "deseq" )
def runEdgeR( infiles, outfile ): '''estimate differential methylation using EdgeR This method applies a paired test. The analysis follows the example in chapter 11 of the EdgeR manual. ''' PipelineWindows.runDE( infiles, outfile, "edger.dir", method = "edger" )