findqtl: Detect a QTL peaks in a QTL profile from (composite) interval...
In behuang/mpMap: Multi-Parent RIL Genetic Analysis

Description Usage Arguments Value See Also Examples

Given the output from a scan of a chromosome, locates local maxima exceeding a significance threshold in a QTL profile.

1	findqtl(mpqtl, dwindow = 5, threshold)

`mpqtl`	Object of class `mpqtl`
`dwindow`	Window over which to smooth p-values - default is five markers
`threshold`	Threshold peaks must exceed to be detected (-log10(p))

The original input object with additional entries for newly detected QTL.

mpIM, plot.mpqtl, summary.mpqtl

sim.map <- qtl::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 <- findqtl(mpq.dat, dwindow=5, threshold=3)
plot(mpq2)
summary(mpq2)