mpestrf: Estimate pairwise recombination fractions between markers

In mpMap: Multi-parent RIL genetic analysis

Description

Estimates pairwise recombination fractions by maximizing the likelihood for a multi-parent cross over a grid of possible values. Theta values and corresponding LOD scores are returned for each pair of markers in the object.

Usage

  mpestrf(object, r, grid = FALSE)

Arguments

object	Object of class mpcross
r	Grid of potential recombination values. If missing the function will maximize over (0, .005, .01, .015, ... , .095, .1, .11, .12, ... .49, .5).
grid	Flag for whether to output the entire grid of likelihoods at each potential recombination value

Value

Returned object is of the class 'mpcross' with the additional component rf. If n.mrk is the number of markers genotypes, this is a list with components:

rf$theta	n.mrk x n.mrk matrix of estimated recombination fractions between each pair of loci
rf$lod	n.mrk x n.mrk matrix of LOD scores at the estimated recombination values
rf$lkhd	n.mrk x n.mrk matrix of likelihood values at the estimated recombination values

See Also

mpcross, plot.mpcross

Examples

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)
plot(dat.rf)

mpMap documentation built on May 29, 2017, 2:50 p.m.