docs/scripts/gs_testmulti.R

In luisgarreta/ppGS: Parallel pipeline for Genomic Selection

#' Create files for multi genomic selection
#'
#' This function creates both parameters file and training/target datasets for genotype/phenotypes 
#' to use them in genomic selection with multiple phenotype (gs_multi).
#' @param outputDir Directory name where files will be saved.
#' @param nGenos (Optional) Number of markers to include in genotype dataset. If empty, use all markers.
#' @param nPhenos (Optional) Number of phenotypes to include in genotype dataset. If empty, use all phenotypes.
#' @return None
#' @export
gs_testmulti <- function (outputDir, nGenos=NA, nPhenos=NA) {
	message (">>> Creating files for Genomic Selection with Multiple phenotypes...")
	createDir (outputDir)
	setwd (outputDir)
	message ("Current dir: ", getwd())
	files = gs_data (sprintf ("%s_datasources", outputDir))
	dataDir = sprintf ("%s_datasets", outputDir)
	gs_split (files$geno, files$phenos, dataDir, nGenos, nPhenos)
	gs_configfile (type="multi", dataDir)
}

#----------------------------------------------------------
# Utility for create dir, if it exists, it is renamed old-XXX
#----------------------------------------------------------
createDir <- function (newDir) {
	checkOldDir <- function (newDir) {
		if (dir.exists (newDir) == T) {
			oldDir = sprintf ("%s/old-%s", dirname (newDir), basename (newDir))
			if (dir.exists (oldDir) == T) checkOldDir (oldDir)
			file.rename (newDir, oldDir)
		}
	}
	checkOldDir (newDir)
	dir.create (sprintf (newDir))
}