The following performs GO term enrichment analysis for each annotated peak set.
args <- systemArgs(sysma="param/macs2.param", mytargets="targets_bam_ref.txt")
args_anno <- systemArgs(sysma="param/annotate_peaks.param", mytargets="targets_macs.txt")
annofiles <- outpaths(args_anno)
gene_ids <- sapply(names(annofiles), function(x) unique(as.character(read.delim(annofiles[x])[,"gene_id"])))
load("data/GO/catdb.RData")
BatchResult <- GOCluster_Report(catdb=catdb, setlist=gene_ids, method="all", id_type="gene", CLSZ=2, cutoff=0.9, gocats=c("MF", "BP", "CC"), recordSpecGO=NULL)