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folds.R |
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| diff -r 53a999633824 -r ec8f372ec8de folds.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/folds.R Fri Oct 21 06:26:15 2016 -0400 |
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| @@ -0,0 +1,49 @@ +######################################################## +# +# creation date : 05/01/16 +# last modification : 27/06/16 +# author : Dr Nicolas Beaume +# owner : IRRI +# +######################################################## + + +############################ helper function #################### + +############################ main function ####################### + +createFolds <- function(nbObs, n) { + index <- sample(1:n, size=nbObs, replace = T) + folds <- NULL + for(i in 1:n) { + folds <- c(folds, list(which(index==i))) + } + return(folds) +} + +############################ main ############################# +# running from terminal (supposing the OghmaGalaxy/bin directory is in your path) : +# folds.sh -i path_to_data [-n nfold] -p phenotype_file [-k nb_classes] -o output_file +## -i : path to the file that contains the genotypes, must be a .rda file (as outputed by loadGenotype.R). +# please note that the table must be called "genotype" when your datafile is saved into .rda (automatic if loadGenotype.R was used) + +## -k : [optional] number of classes of phenotype. This information is used to equilibrate the folds +# if omitted, 2 classes are assumed + +## -p : file that contains the phenotype must be a .rda file (as outputed by loadGenotype.R). +# please note that the table must be called "phenotype" when your datafile is saved into .rda (automatic if loadGenotype.R was used) + +## -n : [optional] number of folds for cross validation. if ommited, n will be setted to 10 + +## -o : path to the file of encoded genotype. the .rda extension is automatically added +cmd <- commandArgs(trailingOnly = T) +source(cmd[1]) +# load data and merge them +con = file(genotype) +genotype <- readLines(con = con, n = 1, ok=T) +close(con) +nObs <- nrow(read.table(genotype, sep="\t", h=T)) +folds <- createFolds(nObs, as.numeric(n)) +out <- paste(out,".rds",sep="") +saveRDS(folds, file=out) +cat(paste(out, "\n", sep="")) \ No newline at end of file |