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.

dir_path <- system.file("extdata/cwl/rundiff", package = "systemPipeR")
args_diff <- loadWF(targets = "targets_countDF.txt", wf_file = "rundiff.cwl", 
    input_file = "rundiff.yml", dir_path = dir_path)
args_diff <- renderWF(args_diff, inputvars = c(FileName = "_FASTQ_PATH1_", 
    SampleName = "_SampleName_"))

cmp <- readComp(file = args_bam, format = "matrix")
dbrlist <- runDiff(args = args_diff, diffFct = run_edgeR, targets = targets.as.df(targets(args_bam)), 
    cmp = cmp[[1]], independent = TRUE, dbrfilter = c(Fold = 2, 
        FDR = 1))
writeTargetsout(x = args_diff, file = "targets_rundiff.txt", 
    step = 1, new_col = "FileName", new_col_output_index = 1, 
    overwrite = TRUE)



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