mpclean: Find Largest Complete mpcross object

In behuang/mpMap: Multi-Parent RIL Genetic Analysis

Description

Finds the largest subset of markers for which all recombination fraction estimates are available for each linkage group. The subsetted object can be returned, or a summary of marker reduction can be given.

Usage

mpclean(object, output.type = c("summary", "object"))

Arguments

object	Object of class mpcross
output.type	Type of output

Value

If the output type is "summary", then a 2 x n.chr matrix is returned. The first row gives the number of markers present on that linkage group. The second row gives the number of markers in the maximal subset. If the output type is "object" then an mpcross object is returned. The object is a subset of the orginial object, with the largest set of markers where all pairs of recombination fractions estimates are availbe in each linkage group.

Examples

map <- qtl::sim.map(len=1, n.mar=30, eq.spacing=FALSE, include.x=FALSE)
sim.ped <- sim.mpped(4, 1, 500, 6, 1)
sim.dat <- sim.mpcross(map=map, pedigree=sim.ped, seed=1)
dat.rf <- mpestrf(sim.dat)
dat.lg<-mpgroup(dat.rf, groups=1)
clean.summary <- mpclean(dat.lg)

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