qtl (version 1.66)

fake.bc: 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.

Author

Karl W Broman,

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.

See Also

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

Examples

data(fake.bc)
fake.bc <- subset(fake.bc,chr=c(2,5,10))
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)