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$new(founderPop)
SP$addTraitA(10)
SP$addSnpChip(5)

#Create population
pop = newPop(founderPop, simParam=SP)
pullSnpGeno(pop, simParam=SP)
#>    1_1 1_2 1_3 1_6 1_11
#> 1    1   0   0   0    1
#> 2    1   0   1   2    0
#> 3    0   1   0   2    2
#> 4    1   1   1   2    1
#> 5    2   1   1   1    1
#> 6    1   1   2   1    2
#> 7    1   1   1   2    1
#> 8    2   0   1   1    0
#> 9    1   1   1   0    2
#> 10   0   1   0   0    1