R/markerlrt.R

In byandell/qtl: Tools for analyzing QTL experiments

######################################################################
#
# 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