mean stability values calcs and replaceBfactor plots

scripts/af_or_calcs.R

@@ -1,17 +1,18 @@
-#!/usr/bin/env Rscript                                                  
-#require('compare')
-require('getopt', quietly=TRUE) # We need to be able to parse arguments
+usr/bin/env Rscript                                                  
+
 #########################################################
 # TASK: To calculate Allele Frequency and
 # Odds Ratio from master data
-# and add the calculated params to meta_data extracted from
-# data_extraction.py
 #########################################################
-#getwd()
+# working dir and loading libraries
+getwd()
 setwd('~/git/LSHTM_analysis/scripts')
 cat(c(getwd(),'\n'))
 
-# Command line args
+# cmd parse arguments
+require('getopt', quietly = TRUE)
+#========================================================
+# command line args
 spec = matrix(c(
   "drug"   , "d", 1, "character",
   "gene"   , "g", 1, "character"
@@ -27,7 +28,7 @@ if(is.null(drug)|is.null(gene)) {
     }
 
 #options(scipen = 999) #disabling scientific notation in R.
-
+#========================================================
 #%% variable assignment: input and output paths & filenames
 gene_match = paste0(gene,'_p.')
 cat(gene_match)