AlphaSimR (version 0.11.1)

pullSegSiteHaplo: Pull seg site haplotypes

Description

Retrieves haplotype data for all segregating sites

Usage

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

Arguments

pop

an object of Pop-class or RawPop-class

haplo

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

chr

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

simParam

an object of SimParam

Value

Returns a matrix of haplotypes

Examples

# NOT RUN {
#Create founder haplotypes
founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)

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

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

# }