# NOT RUN {
data(fake.f2)
# take out several QTLs and make QTL object
qc <- c(1, 8, 13)
qp <- c(26, 56, 28)
fake.f2 <- subset(fake.f2, chr=c(1,2,3,8,13))
# }
# NOT RUN {
fake.f2 <- calc.genoprob(fake.f2, step=2, err=0.001)
qtl <- makeqtl(fake.f2, qc, qp, what="prob")
# scan for an additional QTL
out1 <- addqtl(fake.f2, qtl=qtl, formula=y~Q1+Q2+Q3, method="hk")
max(out1)
# scan for an additional QTL that interacts with the locus on chr 1
out2 <- addqtl(fake.f2, qtl=qtl, formula=y~Q1*Q4+Q2+Q3, method="hk")
max(out2)
# plot interaction LOD scores
plot(out2-out1)
# }
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