annotate randomForest.R @ 56:374c9a2bc1c2 draft

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#
# creation date : 07/01/16
# last modification : 25/10/16
# author : Dr Nicolas Beaume
#
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suppressWarnings(suppressMessages(library(randomForest)))
############################ helper functions #######################
# optimize
optimize <- function(genotype, phenotype, ntree=1000, 
                     rangeMtry=seq(ceiling(ncol(genotype)/5),
                                   ceiling(ncol(genotype)/3), ceiling(ncol(genotype)/100)),
                     repet=3) {
  # accuracy over all mtry values
  acc <- NULL
  for(mtry in rangeMtry) {
    # to compute the mean accuracy over repetiotion for the current mtry value
    tempAcc <- NULL
    for(i in 1:repet) {
      # 1/3 of the dataset is used as test set
      n <- ceiling(nrow(genotype)/3)
      indexTest <- sample(1:nrow(genotype), size=n)
      # create training and test set
      train <- genotype[-indexTest,]
      test <- genotype[indexTest,]
      phenoTrain <- phenotype[-indexTest]
      phenoTest <- phenotype[indexTest]
      # compute model
      model <- randomForest(x=train, y=phenoTrain, ntree = ntree, mtry =mtry)
      # predict on test set and compute accuracy
      pred <- predict(model, test)
      tempAcc <- c(tempAcc, r2(phenoTest, pred))
    }
    # find mean accuracy for the current mtry value
    acc <- c(acc, mean(tempAcc))
  }
  # return mtry for the best accuracy
  names(acc) <- rangeMtry
  bestParam <- which.max(acc)
  return(rangeMtry[bestParam])
}

# 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
r2 <- function(target, prediction) {
  sst <- sum((target-mean(target))^2)
  ssr <- sum((target-prediction)^2)
  return(1-ssr/sst)
}
################################## main function ###########################
rfSelection <- function(genotype, phenotype, folds, outFile, evaluation=T, mtry=NULL, ntree=1000) {
  
  # go for optimization
  if(is.null(mtry)) {
    # find best mtry
    mtry <- seq(ceiling(ncol(genotype)/10), ceiling(ncol(genotype)/3), ceiling(ncol(genotype)/100))
    mtry <- optimize(genotype=genotype, phenotype=phenotype, 
                    ntree = ntree, rangeMtry = mtry)
  }
  # evaluation
  if(evaluation) {
    prediction <- NULL
    for(i in 1:length(folds)) {
      # create training and testing set for the current fold
      train <- genotype[-folds[[i]],]
      test <- genotype[folds[[i]],]
      phenoTrain <- phenotype[-folds[[i]]]
      # compute model
      rf <- randomForest(x=train, y=phenoTrain, mtry = mtry, ntree = ntree)
      # predict and save prediction for the current fold
      prediction <- c(prediction, list(predict(rf, test)))
    }
    # save preductions for all folds to be used for evaluation
    saveRDS(prediction, file = paste(outFile, ".rds", sep = ""))
  } else {
    # just compute the model and save it
    model <- randomForest(x=genotype, y=phenotype, mtry = mtry, ntree=ntree)
    saveRDS(model, file = paste(outFile, ".rds", sep = ""))
  }
}


############################ main #############################
# load parameters
cmd <- commandArgs(T)
source(cmd[1])
# load classifier parameters
mtry <- as.numeric(mtry)
ntree <- as.numeric(ntree)
if(mtry == -1) {mtry <- NULL}
# check if evaluation is required
evaluation <- F
if(as.integer(doEvaluation) == 1) {
  evaluation <- T
  con = file(folds)
  folds <- readLines(con = con, n = 1, ok=T)
  close(con)
  folds <- readRDS(folds)
}
# load genotype and phenotype
con = file(genotype)
genotype <- readLines(con = con, n = 1, ok=T)
close(con)
genotype <- read.table(genotype, sep="\t", h=T)
phenotype <- read.table(phenotype, sep="\t", h=T)[,1] 
# run !
rfSelection(genotype = data.matrix(genotype), phenotype=phenotype,
            evaluation = evaluation, out = out, folds = folds, mtry = mtry, ntree=ntree)
# send the path containing results to galaxy
cat(paste(paste(out, ".rds", sep = ""), "\n", sep=""))