--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/computeR2.R	Fri Oct 28 08:44:42 2016 -0400
@@ -0,0 +1,26 @@
+########################################################
+#
+# creation date : 27/06/16
+# last modification : 22/10/16
+# author : Dr Nicolas Beaume
+# owner : IRRI
+#
+########################################################
+
+# compute r2 by computing the classic formula
+# compare the sum of square difference from target to prediciton
+# to the sum of square difference from target to the mean of the target
+computeR2 <- function(target, prediction) {
+  sst <- sum((target-mean(target))^2)
+  ssr <- sum((target-prediction)^2)
+  return(1-ssr/sst)
+}
+############################ main #############################
+# extract argument
+cmd <- commandArgs(trailingOnly = T)
+source(cmd[1])
+# load target and prediction
+phenotype <- read.table(phenotype, sep="\t", h=T)[,1] 
+predicted <- read.table(predicted, sep = "\t", h=T)[,2]
+# compute r2
+cat(computeR2(phenotype, predicted), file=out)
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