Pull marker genotypes

Retrieves genotype data for user specified loci

Usage

pullMarkerGeno(pop, markers, asRaw = FALSE, simParam = NULL)

Arguments

pop

an object of RawPop-class or MapPop-class

markers

a character vector. Indicates the names of the loci to be retrieved.

asRaw

return in raw (byte) format

simParam

an object of SimParam, not used if pop is MapPop-class

Value

Returns a matrix of 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)

#Pull genotype data for first two markers on chromosome one.
#Marker name is consistent with default naming in AlphaSimR.
pullMarkerGeno(pop, markers=c("1_1","1_2"), simParam=SP)
#>    1_1 1_2
#> 1    1   2
#> 2    1   1
#> 3    2   1
#> 4    1   1
#> 5    2   1
#> 6    1   2
#> 7    0   0
#> 8    2   1
#> 9    1   1
#> 10   1   1