qtl (version 1.70)

listeria: 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.

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)
listeria <- subset(listeria,chr=c(1,5,6,13,15), ind=!is.na(listeria$pheno[,1]))
# 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"))