R: Crude reconstruction of founder haplotypes in multi-parent...

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 `cross`. See `read.cross` for details.
`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)` x no. markers, with the inferred founder origin for each line at each marker.

### Author(s)

Karl W Broman, kbroman@biostat.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")

[Package qtl version 1.41-6 Index]