Pull seg site haplotypes

Retrieves haplotype data for all segregating sites

Usage

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

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

Value

Returns a matrix of haplotypes

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)
pullSegSiteHaplo(pop, simParam=SP)
#>      1_1 1_2 1_3 1_4 1_5 1_6 1_7 1_8 1_9 1_10 1_11 1_12 1_13 1_14 1_15
#> 1_1    0   0   0   0   1   1   0   1   0    0    0    0    0    1    1
#> 1_2    0   1   1   0   0   1   0   0   0    1    0    1    1    1    1
#> 2_1    0   0   0   1   0   0   1   0   1    1    0    1    1    1    1
#> 2_2    1   1   0   0   0   0   0   1   0    0    0    1    1    0    0
#> 3_1    1   1   1   0   0   1   1   1   1    0    0    0    1    0    1
#> 3_2    0   0   0   0   0   0   0   0   1    1    0    0    0    1    1
#> 4_1    1   1   1   0   1   1   1   1   1    0    0    1    1    1    0
#> 4_2    0   1   0   1   0   1   0   0   0    1    0    0    1    0    0
#> 5_1    1   0   1   1   1   1   1   0   1    0    0    1    1    1    1
#> 5_2    1   0   1   1   0   1   0   1   0    1    1    1    0    0    0
#> 6_1    0   0   0   0   0   0   0   0   0    1    0    0    0    1    0
#> 6_2    0   1   0   1   1   1   1   0   0    1    1    1    0    1    0
#> 7_1    1   1   0   0   1   0   1   0   0    0    0    1    0    0    1
#> 7_2    0   1   0   0   1   1   0   1   0    1    1    0    1    0    0
#> 8_1    0   1   0   0   1   0   0   0   1    0    1    1    0    0    1
#> 8_2    1   1   1   0   1   0   0   0   1    1    0    0    0    1    0
#> 9_1    0   0   0   0   1   0   0   1   1    0    1    1    1    0    0
#> 9_2    1   0   1   0   0   1   0   1   1    1    1    1    0    0    1
#> 10_1   1   1   0   1   1   1   1   0   0    1    0    0    0    0    1
#> 10_2   1   0   1   1   1   0   1   0   0    1    1    0    1    0    0