library(qtl)
testmap <- read.cross("csvr", file="SL-F2.csv", estimate.map=FALSE)

summary(testmap)

plot(testmap)


testmap <- calc.genoprob(testmap, step=1)

out.simhk <- scanone(testmap, pheno.col=1, method="hk") 

operm.hk <- scanone (testmap, n.perm=1000, method="hk", pheno.col=1)

summary(out.simhk, perms=operm.hk, alpha=0.05, pvalues=TRUE)

plot(out.simhk, show.marker.names=TRUE)