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######################################################################
#
# countXO.R
#
# copyright (c) 2008-2022, Karl W Broman
# last modified Oct, 2022
# first written Feb, 2008
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License,
# version 3, as published by the Free Software Foundation.
#
# This program is distributed in the hope that it will be useful,
# but without any warranty; without even the implied warranty of
# merchantability or fitness for a particular purpose. See the GNU
# General Public License, version 3, for more details.
#
# A copy of the GNU General Public License, version 3, is available
# at http://www.r-project.org/Licenses/GPL-3
#
# Part of the R/qtl package
# Contains: countXO
#
######################################################################
######################################################################
#
# countXO: Count number of obligate crossovers for each individual
# on individual chromosomes or overall
#
# if bychr=TRUE, return matrix with no. obligate crossovers for each
# individual on each chromosome
# =FALSE, return vector with total no. crossovers across the
# selected chromosomes
######################################################################
countXO <-
function(cross, chr, bychr=FALSE)
{
if(!inherits(cross, "cross"))
stop("Input should have class \"cross\".")
# pull out relevant chromosome
if(!missing(chr)) cross <- subset(cross,chr=chr)
chr.name <- names(cross$geno)
type <- crosstype(cross)
n.ind <- nind(cross)
n.chr <- nchr(cross)
nxo <- matrix(0, ncol=n.chr, nrow=n.ind)
id <- getid(cross)
if(is.null(id)) id <- 1:n.ind
dimnames(nxo) <- list(id, chr.name)
for(i in 1:n.chr) {
chr_type <- chrtype(cross$geno[[i]])
if(chr_type=="X") xchr <- TRUE
else xchr <- FALSE
# which type of cross is this?
if(type == "f2" || type=="bcsft") {
if(!xchr) # autosomal
func <- "R_countXO_f2"
else func <- "R_countXO_bc" # X chromsome
}
else if(type == "bc" || type=="riself" || type=="risib" || type=="dh" || type=="haploid") func <- "R_countXO_bc"
else if(type == "4way") func <- "R_countXO_4way"
else if(type=="ri4self" || type=="ri4sib" || type=="ri8self" || type=="ri8sib" || type=="bgmagic16") {
func <- "R_countXO_ril48"
if(xchr)
warning("countXO not working properly for the X chromosome for 4- or 8-way RIL.")
}
else
stop("ripple not available for cross ", type)
# data to be input
genodat <- cross$geno[[i]]$data
genodat[is.na(genodat)] <- 0
n.mar <- ncol(genodat)
if(n.mar > 1) {
z <- .C(func,
as.integer(n.ind),
as.integer(n.mar),
as.integer(genodat),
oblxo=as.integer(rep(0,n.ind)),
PACKAGE="qtl")
nxo[,i] <- z$oblxo
}
}
if(!bychr) nxo <- apply(nxo, 1, sum)
nxo
}
# end of countXO.R
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