Split phased haplotypes by ancestry

Source: R/ancestry_split.R

Split phased haplotypes deterministically into African and European ancestry-specific dosage matrices. Each haplotype's allele is added to whichever ancestry pool matches its local ancestry call; haplotypes with unrecognised ancestry codes contribute nothing to either pool.

split_haplotype(
  gt_hap0,
  gt_hap1,
  anc_hap0,
  anc_hap1,
  pop_codes = c(AFR = 0L, EUR = 1L)
)

Arguments

gt_hap0

Integer matrix (variants x samples) of haplotype-0 alleles (0/1).

gt_hap1

Integer matrix (variants x samples) of haplotype-1 alleles (0/1).

anc_hap0

Integer matrix (variants x samples) of haplotype-0 ancestry codes.

anc_hap1

Integer matrix (variants x samples) of haplotype-1 ancestry codes.

pop_codes

Named integer vector of length 2 giving the AFR and EUR ancestry codes as used in the MSP file. Defaults to c(AFR = 0L, EUR = 1L) (RFMix convention).

Value

List with two numeric matrices:

african

African ancestry-specific dosage (variants x samples)

european

European ancestry-specific dosage (variants x samples)

Examples

gt0 <- matrix(c(1L, 0L, 0L, 1L), 2, 2)
gt1 <- matrix(c(0L, 1L, 1L, 0L), 2, 2)
a0  <- matrix(c(0L, 1L, 0L, 1L), 2, 2)
a1  <- matrix(c(1L, 0L, 1L, 0L), 2, 2)
split_haplotype(gt0, gt1, a0, a1)
#> $african
#>      [,1] [,2]
#> [1,]    1    0
#> [2,]    1    0
#> 
#> $european
#>      [,1] [,2]
#> [1,]    0    1
#> [2,]    0    1
#>