R/generate-pheno.R

In behuang/mpMap: Multi-Parent RIL Genetic Analysis

#' @importFrom stats rnorm
generate_pheno <- function(n.founders, qtlgeno, qtleffects, vare, n.ind)
{
	pheno <- rnorm(n.ind, 0, vare)
	if (is.null(qtleffects)) return(pheno)
	n.qtl <- nrow(qtleffects)

	for (i in 1:n.qtl)
	{
		for (j in 1:n.founders)
		{
			pheno[qtlgeno[,i]==j] <- pheno[qtlgeno[,i]==j]+qtleffects[i,j+2]
			pheno[qtlgeno[,i+n.qtl]==j] <- pheno[qtlgeno[,i+n.qtl]==j]+qtleffects[i,j+2]  
		}
	}
	return(pheno)
}