Pull SNP genotypes

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$new(founderPop)
SP$nThreads = 1L
SP$addTraitA(10)
SP$addSnpChip(5)

#Create population
pop = newPop(founderPop, simParam=SP)
pullSnpGeno(pop, simParam=SP)
#>    1_1 1_3 1_11 1_14 1_15
#> 1    2   0    1    2    0
#> 2    1   1    1    0    1
#> 3    1   1    1    1    1
#> 4    1   1    0    2    0
#> 5    2   0    1    2    1
#> 6    2   0    1    0    1
#> 7    0   1    2    1    1
#> 8    0   1    2    2    1
#> 9    1   1    1    1    0
#> 10   1   1    0    1    0