pullSnpHaplo {AlphaSimR}

Pull SNP haplotypes

Description

Retrieves SNP haplotype data

Usage

pullSnpHaplo(
  pop,
  snpChip = 1,
  haplo = "all",
  chr = NULL,
  asRaw = FALSE,
  simParam = NULL
)

Arguments

pop

an object of Pop-class

snpChip

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

haplo

either "all" for all haplotypes or an integer for a single set of haplotypes. Use a value of 1 for female haplotypes and a value of 2 for male haplotypes in diploids.

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 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)

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