add fetch args function

1 files changed, 12 insertions, 19 deletions

diff --git a/gn3/computations/biweight.R b/gn3/computations/biweight.R
index 650c5fd..8730536 100644
--- a/gn3/computations/biweight.R
+++ b/gn3/computations/biweight.R
@@ -1,28 +1,21 @@
 
-# library(WGCNA)
+library(WGCNA)
 
+FetchArgs <- function(){
+	myArgs <- commandArgs(trailingOnly = TRUE)
+	trait_vals <- as.numeric(unlist(strsplit(myArgs[1], split=" ")))
+	target_vals <- as.numeric(unlist(strsplit(myArgs[2], split=" ")))
 
-myArgs <- commandArgs(trailingOnly = TRUE)
-trait_vals <- as.numeric(unlist(strsplit(myArgs[1], split=" ")))
-target_vals <- as.numeric(unlist(strsplit(myArgs[2], split=" ")))
+	return(list(trait_vals= c(trait_vals),target_vals = c(target_vals)))
 
-BiweightMidCorrelation <- function(trait_val,target_val){
-    results <- bicorAndPvalue(trait_val,target_val)
-    return (list(c(results$bicor)[1],c(results$p)[1]))
 }
+BiweightMidCorrelation <- function(trait_val,target_val){
 
+	results <- bicorAndPvalue(c(trait_val),c(target_val))
+    return ((c(c(results$bicor)[1],c(results$p)[1])))
+}
 
 
+results <- (BiweightMidCorrelation(FetchArgs()[1],FetchArgs()[2]))
 
-
-
-# the idea is that you get the entire dataset in any format 
-# and then do ther correlation
-
-ComputeAll <-function(trait_val,target_dataset) {
-	for target_val in target_dataset {
-      results = BiweightMidCorrelation(trait_val,target_val)
-      cat(BiweightMidCorrelation(trait_vals,target_vals))
-	}
-}
-
+cat(results)
\ No newline at end of file