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Commit message:
Uploaded |
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added:
computeR2.R |
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| diff -r 8cc5a7448ca6 -r 37d3d073b51d computeR2.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/computeR2.R Fri Oct 28 08:44:42 2016 -0400 |
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| @@ -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) \ No newline at end of file |