Uses groups of adjacent markers to infer the founder haplotypes in SNP data on multi-parent recombinant inbred lines.
inferFounderHap(cross, chr, max.n.markers=15)
An object of class
Indicator of chromosome to consider. If multiple chromosomes are selected, only the first is used.
Maximum number of adjacent markers to consider.
We omit SNPs for which any of the founders are missing.
We then consider groups of adjacent SNPs, looking for founder haplotypes that are unique; RIL sharing such a unique haplotype are then inferred to have that founder's DNA.
We consider each marker as the center of a haplotype, and consider
haplotypes of size 1, 3, 5, ...,
max.n.markers. We end the
extension of the haplotypes when all founders have a unique haplotype.
A matrix of dimension
nind(cross) x no. markers,
with the inferred founder origin for each line at each marker.
Karl W Broman, email@example.com
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map <- sim.map(100, n.mar=101, include.x=FALSE, eq.spacing=TRUE) founderGeno <- simFounderSnps(map, "8") ril <- sim.cross(map, n.ind=10, type="ri8sib", founderGeno=founderGeno) h <- inferFounderHap(ril, max.n.markers=11) mean(!is.na(h)) # proportion inferred plot(map[], h[1,], ylim=c(0.5, 8.5), xlab="Position", ylab="Genotype")