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")