removeHets: Remove heterozygotes

In mpMap2: Genetic Analysis of Multi-Parent Recombinant Inbred Lines

Description

Remove all heterozygotes from dataset

Usage

removeHets()

Details

This function can be used to remove all heterozygotes from an mpcross object. Information about how pairs of different marker alleles are encoded as genotypes is discarded, and all observations of heterozygotes will be marked as NA. Any information calculated based on the genetic data (imputed IBD genotypes, IBD probabilities) will be discarded.

Value

An object of internal class removeHets, which can be combined with an object of class mpcross using the addition operator.

Examples

pedigree <- eightParentPedigreeImproperFunnels(initialPopulationSize = 10,
     selfingGenerations = 1, nSeeds = 1)
#Generate map
map <- qtl::sim.map()
#Simulate data
cross <- simulateMPCross(map = map, pedigree = pedigree, mapFunction = haldane)
finals(cross)[1:5, 1:5]
hetData(cross)[[1]]
cross <- cross + removeHets()
finals(cross)[1:5, 1:5]
hetData(cross)[[1]]

mpMap2 documentation built on Sept. 13, 2020, 5:17 p.m.