biparentalDominant: Make markers in a biparental cross dominant

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

Description

Change the markers in a biparental cross from fully informative to dominant. The dominant founder is chosen randomly for every marker. The transformation is applied to an object using the addition operator, see the example below for details.

Usage

biparentalDominant()

Value

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

Examples

#Simulate an F2 design
f2Pedigree <- f2Pedigree(1000)
map <- qtl::sim.map(len = 100, n.mar = 11, include.x=FALSE)
cross <- simulateMPCross(map = map, pedigree = f2Pedigree, mapFunction = haldane, seed = 1)
founders(cross)
finals(cross)[1:10,]
#The heterozygotes are initially coded as 3
hetData(cross)[[1]]
#Make all markers dominant
dominantCross <- cross + biparentalDominant()
founders(dominantCross)
finals(dominantCross)[1:10,]
#The heterozygotes are now coded the same as one of the homozygotes
hetData(dominantCross)[1:4]

rohan-shah/mpMap2 documentation built on July 21, 2020, 8:58 p.m.