findqtl2: Detect a second QTL in a QTL profile from (composite)...

In behuang/mpMap: Multi-Parent RIL Genetic Analysis

Description

Given the output from an initial scan of chromosomes with significant genetic variation, locates the second peak in a QTL profile.

Usage

findqtl2(mpqtl, window, drop, dwindow = 5)

Arguments

mpqtl	Object of class mpqtl
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

Value

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

See Also

mpIM, plot.mpqtl, summary.mpqtl

Examples

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 <- findqtl2(mpq.dat, drop=2)
plot(mpq2)
summary(mpq2)

behuang/mpMap documentation built on May 12, 2019, 10:53 a.m.