editGenome: Edit genome

In AlphaSimR: Breeding Program Simulations

Edit genome

Description

Edits selected loci of selected individuals to a homozygous state for either the 1 or 0 allele. The gv slot is recalculated to reflect the any changes due to editing, but other slots remain the same.

Usage

editGenome(pop, ind, chr, segSites, allele, simParam = NULL)

Arguments

pop	an object of Pop-class
ind	a vector of individuals to edit
chr	a vector of chromosomes to edit. Length must match length of segSites.
segSites	a vector of segregating sites to edit. Length must match length of chr.
allele	either 0 or 1 for desired allele
simParam	an object of SimParam

Value

Returns an object of Pop-class

Examples

#Create founder haplotypes
founderPop = quickHaplo(nInd=2, nChr=1, segSites=10)

#Set simulation parameters
SP = SimParam$new(founderPop)

SP$addTraitA(10)

#Create population
pop = newPop(founderPop, simParam=SP)

#Change individual 1 to homozygous for the 1 allele 
#at locus 1, chromosome 1
pop2 = editGenome(pop, ind=1, chr=1, segSites=1, 
                  allele=1, simParam=SP)

AlphaSimR documentation built on Nov. 2, 2023, 6:01 p.m.