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" )
