R: Simulated data for a backcross

fake.bc {qtl} | R Documentation

## Simulated data for a backcross

### Description

Simulated data for a backcross, obtained using `sim.cross`.

### Usage

    data(fake.bc)

### Format

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

### Details

There are 400 backcross individuals typed at 91 markers and with two phenotypes and two covariates (sex and age).

The two phenotypes are due to four QTLs, with no epistasis. There is one on chromosome 2 (at 30 cM), two on chromosome 5 (at 10 and 50 cM), and one on chromosome 10 (at 30 cM). The QTL on chromosome 2 has an effect only in the males (sex=1); the two QTLs on chromosome 5 have effect in coupling for the first phenotype and in repulsion for the second phenotype. Age has an effect of increasing the phenotypes.

### Author(s)

Karl W Broman, kbroman@biostat.wisc.edu

### See Also

`sim.cross`, `fake.4way`, `fake.f2`, `listeria`, `hyper`, `bristle3`, `bristleX`

### Examples

    data(fake.bc)

    summary(fake.bc)
    plot(fake.bc)

    # genome scans without covariates
    fake.bc <- calc.genoprob(fake.bc, step=2.5)
    out.nocovar <- scanone(fake.bc, pheno.col=1:2)

    # genome scans with covariates
    ac <- pull.pheno(fake.bc, c("sex","age"))
    ic <- pull.pheno(fake.bc, "sex")
    out.covar <- scanone(fake.bc, pheno.col=1:2,
                          addcovar=ac, intcovar=ic)

    # summaries
    summary(out.nocovar, thr=3, format="allpeaks")
    summary(out.covar, thr=3, format="allpeaks")

    # plots
    plot(out.nocovar, out.covar, chr=c(2,5,10), lod=1, col="blue",
         lty=1:2, ylim=c(0,13))
    plot(out.nocovar, out.covar, chr=c(2,5,10), lod=2, col="red",
         lty=1:2, add=TRUE)

[Package qtl version 1.41-6 Index]