data(fake.bc)
fake.bc <- subset(fake.bc, chr=1:2)
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
if (FALSE) operm.acovar <- scanone(fake.bc, addcovar=ac, n.perm=1000)
operm.acovar <- scanone(fake.bc, pheno.col=1, method="hk", addcovar=ac, n.perm=100)
# re-set the seed
set.seed(theseed)
# permutations with interactive covariate
if (FALSE) operm.icovar <- scanone(fake.bc, addcovar=ac, intcovar=ic,
n.perm=1000)
operm.icovar <- scanone(fake.bc, pheno.col=1, addcovar=ac,
intcovar=ic, method="hk", n.perm=100)
# permutation results for the QTL x covariate interaction
operm.gxc <- operm.icovar - operm.acovar
# LOD thresholds
summary(operm.gxc)
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