perm1+perm2
perm1-perm2

data(fake.bc)

fake.bc <- calc.genoprob(fake.bc, step=2.5)

# covariates
ac <- pull.pheno(fake.bc, c("sex","age"))
ic <- pull.pheno(fake.bc, "sex")

# set seed
theseed <- round(runif(1, 1, 10^8))
set.seed(theseed)

# permutations with additive but not the interactive covariate
## Not run: operm.acovar <- scanone(fake.bc, addcovar=ac, n.perm=1000)


# re-set the seed
set.seed(theseed)

# permutations with interactive covariate
## Not run: operm.icovar <- scanone(fake.bc, addcovar=ac, intcovar=ic,
                      n.perm=1000)

## End(Not run)

# permutation results for the QTL x covariate interaction
operm.gxc <- operm.icovar - operm.acovar

# LOD thresholds
summary(operm.gxc)