AlphaSimR (version 1.6.0)

pullSegSiteHaplo: Pull seg site haplotypes

Description

Retrieves haplotype data for all segregating sites

Usage

pullSegSiteHaplo(
  pop,
  haplo = "all",
  chr = NULL,
  asRaw = FALSE,
  simParam = NULL
)

Value

Returns a matrix of haplotypes

Arguments

pop

an object of RawPop-class or MapPop-class

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, not used if pop is MapPop-class

Examples

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

#Set simulation parameters
SP = SimParam$new(founderPop)
SP$nThreads = 1L
SP$addTraitA(10)
SP$addSnpChip(5)

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