R/wrappers.R

In AgResearch/GUS-LD: Genotyping Uncertainty with Sequencing Data - Linkage Disequilibrium

##########################################################################
# Genotyping Uncertainty with Sequencing data - Linkage Disequilibrium (GUSLD)
# Copyright 2017-2018 AgResearch Ltd. <timothy.bilton@agresearch.co.nz>
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# 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 for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program.  If not, see <http://www.gnu.org/licenses/>.
#########################################################################

#' @useDynLib GUSLD

## likelihood function for LD estimation
ll_gusld <- function(LD, p, ep, ref, alt, nInd){
  epMat <- matrix(ep,nrow=nInd, ncol=2, byrow=TRUE)
  AA <- (1-epMat)^ref*epMat^alt
  AB <- (1/2)^(ref+alt)
  BB <- epMat^ref*(1-epMat)^alt
  ll <- .Call("ll_gusld_c",LD, p, AA, AB, BB, nInd)
  return(-ll)
}