#!/usr/bin/env Rscript require('getopt', quietly=TRUE) spec = matrix(c( "drug" , "d", 1, "character", "gene" , "g", 1, "character" ), byrow=TRUE, ncol=4) opt = getopt(spec); drug = opt$drug gene = opt$gene cat(c('\nDrug:', drug, '\nGene:', gene, '\n'))