BSdat {dlmap}R Documentation

Simulated data for a backcross

Description

Dataset simulated according to Broman and Speed (2002).

Usage

data(BSdat)

Format

An object of class cross. List with two components:

Details

The data was generated for a sample size of 250 from a map with 9 chromosomes. Each chromosome had length 100 cM and contained 11 equally spaced markers (spaced 10 cM apart). The background phenotypic variation was 1.0 and there was no missing data. The QTL were located as follows:

References

Broman, KW and Speed TP. 2002. A model selection approach for the identification of quantitative trait loci in experimental crosses. JRSS-B 64:641-656.

Examples

data(BSdat)
library(qtl) 

# Summary of chromosomes and markers
nchr(BSdat)
nmar(BSdat)

# linkage map of data
plot.map(BSdat)

# interval mapping
BSgp <- calc.genoprob(BSdat, step=2)
BSim <- scanone(BSgp)

# composite interval mapping
BScim <- cim(BSgp, n.marcov=5, method="hk")
 
# LOD profile from CIM
plot(BScim)

# LOD threshold for 5 cofactors from paper
abline(h=3.56)

[Package dlmap version 1.0 Index]