mpestrf: Estimate pairwise recombination fractions between markers

In behuang/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, gpu, lineWeights, mpi = 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).
gpu	Boolean value, true indicates that a GPU should be used if available
lineWeights	In some cases of segregation distortion it can be useful to weight the contribution of each line to the likelihood
mpi	Flag for whether to parallelize the computation
...	Additional arguments to be passed on to mpestrfMpi

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 <- qtl::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)

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