pullSegSiteGeno {AlphaSimR}

Pull segregating site genotypes

Description

Retrieves genotype data for all segregating sites

Usage

pullSegSiteGeno(pop, chr = NULL, asRaw = FALSE, simParam = NULL)

Arguments

pop

an object of RawPop-class or MapPop-class

chr

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

asRaw

return in raw (byte) format

simParam

an object of SimParam, not used if pop is MapPop-class

Value

Returns a matrix of genotypes

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)

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