mpMap (version 1.14)

mpgroup: Group markers into linkage groups given 2-pt recombination fraction estimates

Description

Groups markers based on estimated pairwise recombination fractions. Linkage groups are built up by adding a marker if it satisfies the criteria for linkage with at least one other marker in the group.

Usage

mpgroup(mpcross, theta = 0.15, LOD = 5)

Arguments

mpcross

an object of class mpcross which includes the component rf output by mp.est.rf. See mpcross.object for further details.

theta

Threshold for grouping based on recombination fraction value

LOD

Threshold for grouping based on LOD score value

Value

The original object, with the added component lg which is a list with the following components:

n.groups

The number of linkage groups formed by the function

groups

Vector labelling each marker by assigned linkage group. Missing values mean that the marker was linked to more than one group and could not be assigned with confidence

LODthresh

The LOD threshold value used to determine linkage

thetathresh

The theta threshold value used to determine linkage

order

A list with a component for each constructed linkage group which contains the order of the markers within the linkage group

See Also

mpestrf

map <- sim.map(len=100, n.mar=11, eq.spacing=TRUE, include.x=FALSE) sim.ped <- sim.mpped(4, 1, 500, 6, 1) sim.dat <- sim.mpcross(map=map, pedigree=sim.ped, qtl=matrix(data=c(1, 50, .4, 0, 0, 0), nrow=1, ncol=6, byrow=TRUE), seed=1) dat.rf <- mpestrf(sim.dat) dat.lg <- mpgroup(dat.rf)