Convert letter genotypes to allele dosages

Accepts two-letter calls (AA, AG), separated calls (A/G, A|G) and single IUPAC codes (A, R, Y, ...). For each marker the most common allele is the reference, so a dosage counts copies of the other allele: 0 = homozygous for the common allele, 1 = heterozygous, 2 = homozygous for the other allele. Markers with more than two alleles count every allele that is not the common one.

Usage

genotypes_to_dosage(m)

Arguments

m

Character matrix with samples in rows and markers in columns.

Value

Numeric matrix of 0, 1, 2 and NA, same dimensions as m.

Examples

genotypes_to_dosage(matrix(c("AA", "AG", "GG", "R", "NN", "A/G"), 3))
#>      [,1] [,2]
#> [1,]    0    1
#> [2,]    1   NA
#> [3,]    2    1