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######################################################################
#
# markerlrt.R
#
# copyright (c) 2010, Karl W Broman
# last modified Jul, 2010
# first written Jul, 2010
#
# 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: markerlrt
#
######################################################################
######################################################################
#
# markerlrt: General likelihood ratio test to assess linkage between
# all pairs of markers
#
######################################################################
markerlrt <-
function(cross)
{
if(!any(class(cross) == "cross"))
stop("Input should have class \"cross\".")
Geno <- pull.geno(cross)
Geno[is.na(Geno)] <- 0
maxg <- max(as.numeric(Geno))
n.ind <- nrow(Geno)
n.mar <- ncol(Geno)
mar.names <- colnames(Geno)
z <- .C("R_markerlrt",
as.integer(n.ind), # number of individuals
as.integer(n.mar), # number of markers
as.integer(Geno),
as.integer(maxg), # maximum observed genotype
lod = as.double(rep(0,n.mar*n.mar)),
PACKAGE="qtl")
cross$rf <- matrix(z$lod,ncol=n.mar)
dimnames(cross$rf) <- list(mar.names,mar.names)
attr(cross$rf, "onlylod") <- TRUE
cross
}
# end of markerlrt.R
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