pullSnpGeno {AlphaSimR}

Pull SNP genotypes

Description

Retrieves SNP genotype data

Usage

pullSnpGeno(pop, snpChip = 1, chr = NULL, asRaw = FALSE, simParam = NULL)

Arguments

pop

an object of Pop-class

snpChip

an integer. Indicates which SNP chip's genotypes to retrieve.

chr

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

asRaw

return in raw (byte) format

simParam

an object of SimParam

Value

Returns a matrix of SNP 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)
pullSnpGeno(pop, simParam=SP)