Description Usage Arguments Value See Also Examples
Given the output from an initial scan of chromosomes with significant genetic variation, locates the second peak in a QTL profile.
1 |
mpqtl |
Object of class |
window |
cM on each side of initial QTL from which to exclude second peak |
drop |
Drop from original peak required in order to detect a second peak which is above the significance threshold |
dwindow |
Window over which to smooth p-values - default is five markers |
The original input object with additional entries for newly detected QTL.
mpIM
,
plot.mpqtl
,
summary.mpqtl
1 2 3 4 5 6 7 8 | sim.map <- sim.map(len=rep(100, 2), n.mar=11, include.x=FALSE, eq.spacing=TRUE)
sim.ped <- sim.mpped(4, 1, 500, 6, 1)
sim.dat <- sim.mpcross(map=sim.map, pedigree=sim.ped, qtl=matrix(data=c(1, 10, .4, 0, 0, 0, 1, 70, 0, .35, 0, 0), nrow=2, ncol=6, byrow=TRUE), seed=1)
mpp.dat <- mpprob(sim.dat, program="qtl", step=2)
mpq.dat <- mpIM(object=mpp.dat, ncov=0, responsename="pheno")
mpq2 <- findqtl2(mpq.dat, drop=2)
plot(mpq2)
summary(mpq2)
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