R: Simulated data for a 4-way cross

fake.4way {qtl} | R Documentation

## Simulated data for a 4-way cross

### Description

Simulated data for a phase-known 4-way cross, obtained using `sim.cross`.

### Usage

    data(fake.4way)

### Format

An object of class `cross`. See `read.cross` for details.

### Details

There are 250 individuals typed at 157 markers, including 8 on the X chromosome.

There are two phenotypes (including sex, for which 0=female and 1=male). The quantitative phenotype is affected by three QTLs: two on chromosome 2 at positions 10 and 25 cM on the female genetic map, and one on chromosome 7 at position 40 cM on the female map.

### Author(s)

Karl W Broman, kbroman@biostat.wisc.edu

### See Also

`sim.cross`, `fake.bc`, `fake.f2`, `listeria`, `hyper`, `bristle3`, `bristleX`

### Examples

    data(fake.4way)

    plot(fake.4way)
    summary(fake.4way)

    # estimate recombination fractions
    fake.4way <- est.rf(fake.4way)
    plotRF(fake.4way)

    # estimate genetic maps
    ssmap <- est.map(fake.4way, verbose=TRUE)
    samap <- est.map(fake.4way, sex.sp=FALSE, verbose=TRUE)
    plot(ssmap, samap)

    # error lod scores
    fake.4way <- calc.genoprob(fake.4way, err=0.01)
    fake.4way <- calc.errorlod(fake.4way, err=0.01)
    top.errorlod(fake.4way, cutoff=2.5)

    # genome scan
    fake.4way <- calc.genoprob(fake.4way, step=2.5)
    out.hk <- scanone(fake.4way, method="hk")
    out.em <- scanone(fake.4way, method="em")
    plot(out.em,out.hk,chr=c(2,7))

[Package qtl version 1.41-6 Index]