Simulated data for a backcross
Simulated data for a backcross, obtained using
sim.cross.
data(fake.bc)
An object of class cross. See read.cross
for 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.
Karl W Broman, broman@wisc.edu
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)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.