Crude reconstruction of founder haplotypes in multi-parent RIL
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)
cross |
An object of class |
chr |
Indicator of chromosome to consider. If multiple chromosomes are selected, only the first is used. |
max.n.markers |
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, broman@wisc.edu
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[[1]], h[1,], ylim=c(0.5, 8.5), xlab="Position", ylab="Genotype")
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