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#####################################################################
#
# inferFounderHap.R
#
# copyright (c) 2011, Karl W Broman
# last modified Dec, 2011
# first written Dec, 2011
#
# 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: inferFounderHap, restoreMWrilGeno
#
# This is for reconstructing the founder haplotypes in inbred lines
# by a crude method using groups of adjacent SNPs
#
######################################################################
inferFounderHap <-
function(cross, chr, max.n.markers=15)
{
if(!missing(chr))
cross <- subset(cross, chr=chr)
if(nchr(cross) > 1) {
thechr <- names(cross$geno)[1]
cross <- subset(cross, chr=thechr)
warning("inferFounderHap is only for one chromosome; considering ", thechr)
}
# pull out genotypes for RIL and founders
offspringGen <- restoreMWrilGeno(cross)
founderGen <- cross$founderGeno
# drop markers with any missing data in the founders
nomissing <- apply(founderGen, 2, function(a) !any(is.na(a)))
names(nomissing) <- colnames(offspringGen)
if(!any(nomissing))
stop("No markers with complete founder genotypes")
offspringGen <- offspringGen[,nomissing,drop=FALSE]
founderGen <- founderGen[,nomissing,drop=FALSE]
longbits <- .Machine$sizeof.long*8
if(max.n.markers > longbits-1) {
max.n.markers <- longbits-1
warning("We can't use max.n.markers > ", longbits-1,
", so we're taking max.n.markers = ", longbits-1)
}
n.mar <- ncol(offspringGen)
if(max.n.markers > n.mar) max.n.markers <- n.mar
max.offset <- ceiling((max.n.markers-1)/2)
n.ind <- nrow(offspringGen)
n.founders <- nrow(founderGen)
if(n.mar != ncol(founderGen))
stop("ncol(offspringGen) != ncol(founderGen)")
if(any(!is.na(offspringGen) & offspringGen != 0 & offspringGen != 1))
stop("offspringGen should be NA, 0 or 1")
if(any(!is.na(founderGen) & founderGen != 0 & founderGen != 1))
stop("founderGen should be NA, 0 or 1")
offspringGen[is.na(offspringGen)] <- -1
z <- .C("R_inferFounderHap",
as.integer(n.mar),
as.integer(n.founders),
as.integer(n.ind),
as.integer(founderGen),
as.integer(offspringGen),
as.integer(max.offset),
hap=as.integer(rep(0,n.mar * n.ind)),
PACKAGE="qtl")
z$hap[z$hap <= 0] <- NA
fullhap <- matrix(ncol=length(nomissing), nrow=n.ind)
fullhap[,nomissing] <- matrix(z$hap, ncol=n.mar, nrow=n.ind)
colnames(fullhap) <- names(nomissing)
fullhap
}
restoreMWrilGeno <-
function(cross)
{
g <- pull.geno(cross)
f <- cross$founderGeno
uf <- unique(as.numeric(f[!is.na(f)]))
f[is.na(f)] <- missingval <- min(uf)-1
g[is.na(g)] <- 0
n.mar <- ncol(g)
n.ind <- nrow(g)
n.str <- nrow(f)
if(n.mar != ncol(f))
stop("no. genotypes inconsistent between offspring and founders.")
crosses <- cross$cross
if(ncol(crosses) != n.str || nrow(crosses) != n.ind)
stop("Incompatiability in cross$cross dimension.")
gen <-
.C("R_restoreMWrilGeno",
as.integer(n.ind),
as.integer(n.mar),
as.integer(n.str),
as.integer(f),
gen=as.integer(g),
as.integer(crosses),
as.integer(missingval),
PACKAGE="qtl")$gen
gen[gen==missingval] <- NA
gen <- matrix(gen, nrow=n.ind, ncol=n.mar)
colnames(gen) <- colnames(g)
gen
}
# end of inferFounderHap.R
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