Pull IBD haplotypes

Retrieves IBD haplotype data

Usage

pullIbdHaplo(pop, chr = NULL, snpChip = NULL, simParam = NULL)

Arguments

pop

an object of Pop-class

chr

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

snpChip

an integer indicating which SNP array loci are to be retrieved. If NULL, all sites are retrieved.

simParam

an object of SimParam

Value

Returns a matrix of IBD haplotypes.

Examples

#Create founder haplotypes
founderPop = quickHaplo(nInd=10, nChr=1, segSites=15)

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

#Create population
pop = newPop(founderPop, simParam=SP)
pullIbdHaplo(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    1   1   1   1   1   1   1   1   1    1    1    1    1    1    1
#> 1_2    2   2   2   2   2   2   2   2   2    2    2    2    2    2    2
#> 2_1    3   3   3   3   3   3   3   3   3    3    3    3    3    3    3
#> 2_2    4   4   4   4   4   4   4   4   4    4    4    4    4    4    4
#> 3_1    5   5   5   5   5   5   5   5   5    5    5    5    5    5    5
#> 3_2    6   6   6   6   6   6   6   6   6    6    6    6    6    6    6
#> 4_1    7   7   7   7   7   7   7   7   7    7    7    7    7    7    7
#> 4_2    8   8   8   8   8   8   8   8   8    8    8    8    8    8    8
#> 5_1    9   9   9   9   9   9   9   9   9    9    9    9    9    9    9
#> 5_2   10  10  10  10  10  10  10  10  10   10   10   10   10   10   10
#> 6_1   11  11  11  11  11  11  11  11  11   11   11   11   11   11   11
#> 6_2   12  12  12  12  12  12  12  12  12   12   12   12   12   12   12
#> 7_1   13  13  13  13  13  13  13  13  13   13   13   13   13   13   13
#> 7_2   14  14  14  14  14  14  14  14  14   14   14   14   14   14   14
#> 8_1   15  15  15  15  15  15  15  15  15   15   15   15   15   15   15
#> 8_2   16  16  16  16  16  16  16  16  16   16   16   16   16   16   16
#> 9_1   17  17  17  17  17  17  17  17  17   17   17   17   17   17   17
#> 9_2   18  18  18  18  18  18  18  18  18   18   18   18   18   18   18
#> 10_1  19  19  19  19  19  19  19  19  19   19   19   19   19   19   19
#> 10_2  20  20  20  20  20  20  20  20  20   20   20   20   20   20   20