qtlmap: Select markers in a region around QTL

In behuang/mpMap: Multi-Parent RIL Genetic Analysis

Description

Outputs a list of markers in regions around QTL. Region is defined by the window parameter of x cM to either side of the QTL positions.

Usage

qtlmap(qtlpos, qtlchr, map, window = 10, qtlnam)

Arguments

qtlpos	Vector of QTL positions
qtlchr	Vector of QTL chromosomes (one for each position)
map	Linkage map to determine where QTL are relative to other markers
window	Number of cM to each side of QTL in which to find nearby markers
qtlnam	Optional vector of names for the QTL

Value

Returns a map selecting out regions +- window around the QTL positions.

See Also

plotlink.map

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")
mpq.dat <- mpIM(object=mpp.dat, ncov=0, responsename="pheno")
qmap <- qtlmap(summary(mpq.dat)[,2], summary(mpq.dat)[,1], mpq.dat$map)
plotlink.map(qmap)

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