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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 : 27/06/16
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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 log <- file(paste(getwd(), "log_computeR2.txt", sep="/"), open = "wt")
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11 sink(file = log, type="message")
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12
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13 library("miscTools")
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14 library(randomForest)
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15
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16 computeR2 <- function(phenotype, prediction) {
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17 return(rSquared(phenotype, (phenotype - prediction))[1,1])
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18 }
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19 ############################ main #############################
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20 cmd <- commandArgs(trailingOnly = T)
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21 source(cmd[1])
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22 phenotype <- read.table(phenotype, sep="\t", h=T)[,1]
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23 predicted <- read.table(predicted, sep = "\t", h=T)[,2]
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24 cat(computeR2(phenotype, predicted), file=out) |
