fix script path issues

1 files changed, 16 insertions, 3 deletions

diff --git a/gn3/computations/biweight.R b/gn3/computations/biweight.R
index 05f7145..650c5fd 100644
--- a/gn3/computations/biweight.R
+++ b/gn3/computations/biweight.R
@@ -1,5 +1,5 @@
 
-library(WGCNA)
+# library(WGCNA)
 
 
 myArgs <- commandArgs(trailingOnly = TRUE)
@@ -7,9 +7,22 @@ trait_vals <- as.numeric(unlist(strsplit(myArgs[1], split=" ")))
 target_vals <- as.numeric(unlist(strsplit(myArgs[2], split=" ")))
 
 BiweightMidCorrelation <- function(trait_val,target_val){
-    results <- bicorAndPvalue(x,y)
+    results <- bicorAndPvalue(trait_val,target_val)
     return (list(c(results$bicor)[1],c(results$p)[1]))
 }
-cat(BiweightMidCorrelation(trait_vals,target_vals))
 
 
+
+
+
+
+# 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))
+	}
+}
+