R: Data on Listeria monocytogenes susceptibility

listeria {qtl} | R Documentation

## Data on Listeria monocytogenes susceptibility

### Description

Data from an experiment on susceptibility to Listeria monocytogenes infection in the mouse.

### Usage

    data(listeria)

### Format

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

### Details

There are 120 F2 individuals typed at 133 markers, including 2 on the X chromosome, with one phenotype.

The phenotype is the survival time (in hours) following infection. Mice with phenotype 264 hours may be considered to have recovered from the infection. See the references below.

### Source

Victor Boyartchuk and William Dietrich (Department of Genetics, Harvard Medical School and Howard Hughes Medical Institute)

### References

Boyartchuk, V. L., Broman, K. W., Mosher, R. E., D'Orazio S. E. F., Starnbach, M. N. and Dietrich, W. F. (2001) Multigenic control of Listeria monocytogenes susceptibility in mice. Nature Genetics 27, 259–260.

Broman, K. W. (2003) Mapping quantitative trait loci in the case of a spike in the phenotype distribution. Genetics 163, 1169–1175.

### See Also

`fake.bc`, `fake.f2`, `fake.4way`, `hyper`, `bristle3`, `bristleX`

### Examples

    data(listeria)

    # Summaries
    summary(listeria)
    plot(listeria)

    # Take log of phenotype
    listeria$pheno[,1] <- log2(listeria$pheno[,1])
    plot(listeria)

    # Genome scan with a two-part model, using log survival
    listeria <- calc.genoprob(listeria, step=2)
    out <- scanone(listeria, model="2part", method="em",
                   upper=TRUE)

    # Summary of the results
    summary(out, thr=c(5,3,3), format="allpeaks")

    # Plot LOD curves for interesting chromosomes
    #     (The two-part model gives three LOD scores)
    plot(out, chr=c(1,5,6,13,15), lodcolumn=1:3,
         lty=1, col=c("black","red","blue"))

[Package qtl version 1.41-6 Index]