R: Simulate founder SNPs for a multiple-strain RIL

simFounderSnps {qtl} | R Documentation

## Simulate founder SNPs for a multiple-strain RIL

### Description

Simulate genotype data for the founding strains for a panel of multiple-strain RIL.

### Usage

    simFounderSnps(map, n.str=c("4","8"), pat.freq)

### Arguments

`map` | A list whose components are vectors containing the marker locations on each of the chromosomes.
`n.str` | Number of founding strains (4 or 8).
`pat.freq` | Frequency of SNP genotype patterns in the founder (a vector of length `n.str`/2 + 1): (monoallelic, SNP unique to one founder, SNP present in 2 founders, [and, for the case of 8 founders, SNP in 3/8 founders, SNP in 4/8 founders].)

### Details

The SNPs are simulated to be in linkage equilibrium.

### Value

A vector of the same length as there are chromosomes in `map`, with each component being a matrix of 0's and 1's, of dim `n.str` x `n.mar`.

### Author(s)

Karl W Broman, kbroman@biostat.wisc.edu

### See Also

`sim.map`, `sim.cross`

### Examples

    data(map10)
    x <- simFounderSnps(map10, "8", c(0, 0.5, 0.2, 0.2, 0.1))

[Package qtl version 1.41-6 Index]