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RNAseq_6_enrichfunc.R

 	make_option(c("-q", "--qvalueCutoff"), type="double",default=0.2,metavar="number",
 		help="Cutoff value of q value. [default: 0.2]"),
    	make_option(c("-p", "--project_code"), type="character",default="rnaseq",
-        help="Project code, which is used as prefix of output file. [default: rnaseq]")
+        help="Project code, which is used as prefix of output file. [default: rnaseq]"),
+	make_option(c("-d", "--ref_rdata_dir"), type="character",default="./",
+        help="The directory of reference files: human_c2_v5p2.rdata, human_c5_v5p2.rdata and ID_convert_table.rds. [default: ./]")
 		)
 
+
 # get command line options, if help option encountered print help and exit,
 # otherwise if options not found on command line then set defaults, 
 opt <- parse_args(OptionParser(option_list=option_list))
 
 message("Begin ID conversion.")
 
-if(length(grep("ID_convert_table.rds",dir()))>0){
-idconvert<-readRDS("ID_convert_table.rds")
+refdir<-paste(gsub("/$","",opt$ref_rdata_dir),"/",sep="")
+
+if(length(grep("ID_convert_table.rds",dir(refdir)))>0){
+idconvert<-readRDS(paste(refdir,"ID_convert_table.rds",sep=""))
 }else{
- stop("Cannot find ID_convert_table.rds in the working folder. Exit!", call.=FALSE)
+ stop("Cannot find ID_convert_table.rds in the ref_rdata_dir. Exit!", call.=FALSE)
 }
 
 if(opt$type_gene_id=="EnsemblGID"){