The runDiff function performs differential binding analysis in batch mode for several count tables using edgeR or DESeq2 (Robinson et al., 2010; Love et al., 2014). Internally, it calls the functions run_edgeR and run_DESeq2. It also returns the filtering results and plots from the downstream filterDEGs function using the fold change and FDR cutoffs provided under the dbrfilter argument.

args_diff <- systemArgs(sysma="param/rundiff.param", mytargets="targets_countDF.txt")
cmp <- readComp(file=args_bam, format="matrix") 
dbrlist <- runDiff(args=args_diff, diffFct=run_edgeR, targets=targetsin(args_bam), 
                    cmp=cmp[[1]], independent=TRUE, dbrfilter=c(Fold=2, FDR=1))
writeTargetsout(x=args_diff, file="targets_rundiff.txt", overwrite=TRUE)
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