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1
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2 ########################################################
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3 #
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4 # creation date : 05/01/16
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5 # last modification : 25/10/16
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6 # author : Dr Nicolas Beaume
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7 #
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8 ########################################################
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9
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10
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11 library(rrBLUP)
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12 ############################ helper functions #######################
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13
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14
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15 ################################## main function ###########################
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16 # do rrBLUP evaluation of classification.
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17 # optimization of paramaters is included in rrBLUP package
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18 rrBLUP <- function(genotype, phenotype, outFile, evaluation=F, folds) {
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19 # Evaluation mode
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20 if(evaluation) {
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21 prediction <- NULL
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22 # run over folds
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23 for(i in 1:length(folds)) {
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24 # create training and test set for this fold
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25 train <- genotype[-folds[[i]],]
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26 test <- genotype[folds[[i]],]
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27 phenoTrain <- phenotype[-folds[[i]]]
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28 phenoTest <- phenotype[folds[[i]]]
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29 # create model
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30 model <-mixed.solve(phenoTrain, Z=train,K=NULL, SE=F,return.Hinv = F)
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31 # predict current test set
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32 pred <- as.matrix(test) %*% as.matrix(model$u)
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33 pred <- pred[,1]+model$beta
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34 prediction <- c(prediction, list(pred))
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35 }
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36 # save results
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37 saveRDS(prediction, file=paste(outFile,".rds", sep=""))
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38 # just create a model
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39 } else {
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40 # create and save modle
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41 model <-mixed.solve(phenotype, Z=genotype,K=NULL, SE=F,return.Hinv = F)
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42 saveRDS(model, file = paste(outFile, ".rds", sep = ""))
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43 }
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44 }
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45
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46
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47 ############################ main #############################
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48 # get argument from xml file
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49 cmd <- commandArgs(T)
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50 source(cmd[1])
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51 # for evaluation mode : set evaluation as True and load fold file
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52 if(as.integer(evaluation) == 1) {
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53 evaluation <- T
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54 con = file(folds)
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55 folds <- readLines(con = con, n = 1, ok=T)
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56 close(con)
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57 folds <- readRDS(folds)
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58 } else{
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59 evaluation <- F
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60 }
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61 # load genotype and phenotype
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62 con = file(genotype)
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63 genotype <- readLines(con = con, n = 1, ok=T)
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64 close(con)
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65 genotype <- read.table(genotype, sep="\t", h=T)
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66 phenotype <- read.table(phenotype, sep="\t", h=T)[,1]
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67 # run !
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68 rrBLUP(genotype = genotype, phenotype = phenotype, outFile = out,
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69 evaluation = evaluation, folds = folds)
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70 # return path of the result to galaxy
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71 cat(paste(paste(out, ".rds", sep = ""), "\n", sep="")) |
