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comparison computeR2.R @ 71:37d3d073b51d draft

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author nicolas
date Fri, 28 Oct 2016 08:44:42 -0400
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70:8cc5a7448ca6 71:37d3d073b51d
1 ########################################################
2 #
3 # creation date : 27/06/16
4 # last modification : 22/10/16
5 # author : Dr Nicolas Beaume
6 # owner : IRRI
7 #
8 ########################################################
9
10 # compute r2 by computing the classic formula
11 # compare the sum of square difference from target to prediciton
12 # to the sum of square difference from target to the mean of the target
13 computeR2 <- function(target, prediction) {
14 sst <- sum((target-mean(target))^2)
15 ssr <- sum((target-prediction)^2)
16 return(1-ssr/sst)
17 }
18 ############################ main #############################
19 # extract argument
20 cmd <- commandArgs(trailingOnly = T)
21 source(cmd[1])
22 # load target and prediction
23 phenotype <- read.table(phenotype, sep="\t", h=T)[,1]
24 predicted <- read.table(predicted, sep = "\t", h=T)[,2]
25 # compute r2
26 cat(computeR2(phenotype, predicted), file=out)