pullIbdHaplo {AlphaSimR}

Pull IBD haplotypes

Description

Retrieves IBD haplotype data

Usage

pullIbdHaplo(pop, chr = NULL, snpChip = NULL, simParam = NULL)

Arguments

pop

an object of Pop-class

chr

a vector of chromosomes to retrieve. If NULL, all chromosomes are retrieved.

snpChip

an integer indicating which SNP array loci are to be retrieved. If NULL, all sites are retrieved.

simParam

an object of SimParam

Value

Returns a matrix of IBD haplotypes.

Examples

#Create founder haplotypes
founderPop = quickHaplo(nInd=10, nChr=1, segSites=15)

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

SP$addTraitA(10)
SP$addSnpChip(5)
SP$setTrackRec(TRUE)

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