inferFounderHap {qtl} | R Documentation |
Crude reconstruction of founder haplotypes in multi-parent RIL
Description
Uses groups of adjacent markers to infer the founder haplotypes in SNP data on multi-parent recombinant inbred lines.
Usage
inferFounderHap(cross, chr, max.n.markers=15)
Arguments
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. |
Details
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.
Value
A matrix of dimension nind(cross)
\times
no. markers,
with the inferred founder origin for each line at each marker.
Author(s)
Karl W Broman, broman@wisc.edu
See Also
sim.geno
, calc.genoprob
,
fill.geno
, argmax.geno
Examples
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")