R/getAllFunnels.R

In behuang/mpMap: Multi-Parent RIL Genetic Analysis

getAllFunnels <- function(mpcross)
{
	if(class(mpcross$founders) != "matrix") mpcross$founders <- as.matrix(mpcross$founders)
	if(class(mpcross$finals) != "matrix") mpcross$finals <- as.matrix(mpcross$finals)
	
	if(mode(mpcross$fid) == "numeric") mode(mpcross$fid) <- "integer"
	if(mode(mpcross$id) == "numeric") mode(mpcross$id) <- "integer"
	if(mode(mpcross$founders) == "numeric") mode(mpcross$founders) <- "integer"
	if(mode(mpcross$finals) == "numeric") mode(mpcross$finals) <- "integer"
	if(!inherits(mpcross, "mpcross")) stop("Input must have class mpcross")
	funnels <- .Call("getAllFunnels", mpcross, PACKAGE="mpMap")

	if (ncol(funnels)==4) colnames(funnels) <- c("ff", "mf", "fm", "mm")
	if (ncol(funnels)==8) colnames(funnels) <- c("fff", "mff", "fmf", "mmf", "ffm", "mfm", "fmm", "mmm")
	if (ncol(funnels)==16) colnames(funnels) <- c("ffff", "mfff", "fmff", "mmff", "ffmf", "mfmf", "fmmf", "mmmf", "fffm", "mffm", "fmfm", "mmfm", "ffmm", "mfmm", "fmmm", "mmmm")

	return(funnels)
}