getopt and commandArgs examples, and AF/OR update to use getopt()

scripts/getopt-example.r

@@ -0,0 +1,14 @@
+#!/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'))