Nothing
#####################################################################
#
# addmarker.R
#
# copyright (c) 2013-2019, Karl W Broman
# last modified Dec, 2019
# first written May, 2013
#
# 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: addmarker.R
######################################################################
######################################################################
# add a marker to a cross object
#
# cross: the cross object
# genotypes: vector of numeric genotypes
# markername: character string with the marker name
# chr: character string with the chromosome ID
# pos: position of the marker
######################################################################
addmarker <-
function(cross, genotypes, markername, chr, pos)
{
if(!inherits(cross, "cross"))
stop("cross must have class \"cross\"")
chr <- matchchr(chr, names(cross$geno))
if(length(chr) != 1)
stop("Only 1 chromosome should be specified.")
if(length(pos) != 1)
stop("length(pos) != 1: length(pos) = ", length(pos))
if(length(markername) != 1)
stop("length(markername) != 1: length(markername) = ", length(markername))
if(length(genotypes) != nind(cross))
stop("length(genotypes) != nind(cross): length(genotypes) = ", length(genotypes),
", nind(cross) = ", nind(cross))
map <- cross$geno[[chr]]$map
where <- sum(map < pos)
g <- cross$geno[[chr]]$data
if(where == 0) {
map <- c("tmp"=pos, map)
names(map)[1] <- markername
cross$geno[[chr]]$map <- map
g <- cbind("tmp"=genotypes, g)
colnames(g)[1] <- markername
cross$geno[[chr]]$data <- g
}
else if(where == length(map)) {
map <- c(map,"tmp"=pos)
names(map)[length(map)] <- markername
cross$geno[[chr]]$map <- map
g <- cbind(g, "tmp"=genotypes)
colnames(g)[length(map)] <- markername
cross$geno[[chr]]$data <- g
}
else {
mnames <- names(map)
map <- c(map[1:where], "tmp"=pos, map[-(1:where)])
names(map) <- c(mnames[1:where], markername, mnames[-(1:where)])
cross$geno[[chr]]$map <- map
g <- cbind(g[,1:where, drop=FALSE], genotypes, g[,-(1:where), drop=FALSE])
colnames(g) <- names(map)
cross$geno[[chr]]$data <- g
}
cross
}
# end of addmarker.R
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