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