data(fake.bc)
fake.bc <- subset(fake.bc, chr=c(2,5))
fake.bc <- calc.genoprob(fake.bc, step=2)
qtl <- makeqtl(fake.bc, chr=c(2,5), pos=c(32.5, 17.5), what="prob")
out <- scanone(fake.bc, method="hk")
# refine QTL positions and keep LOD profiles
rqtl <- refineqtl(fake.bc, qtl=qtl, method="hk", keeplodprofile=TRUE)
# plot the LOD profiles
plotLodProfile(rqtl)
# add the initial scan results, for comparison
plot(out, add=TRUE, chr=c(2,5), col="red")
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