mpMap (version 1.14)

qtlmap: Select markers in a region around QTL

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 <- 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)