Count the number of alleles for each locus in an HLA typing string

count_alleles() takes in a character vector or string of HLA typings, and returns the number of alleles that the string contains for each locus.

This can be useful when validating whether a typing string contains a typing for each locus. Also, this function can alert you when a typing string contains more than two alleles for each locus, which can be intentional (e.g. when the typing contains both the broad and the split) or a mistake.

Usage

count_alleles(
  typings,
  loci = c("A", "B", "C", "DPA1", "DPB1", "DQA1", "DQB1", "DRB1", "DRB.")
)

Arguments

typings

A(n) (character vector of) HLA typing string(s).

loci

A string or character vector with the loci you are interested in. Only these alleles will be returned. Defaults to all. DRB. is used for DRB3, DRB4, and DRB5.

Value

A (list of) named integer vector(s), with the loci as names, and the number of found alleles per locus as values.

Examples

typing <- "A1 A2 B7 B8 Cw3 DQ5 DQ8 DR4 DR11 DR52 DR53"
count_alleles(typing, loci = "A")
#> A 
#> 2 
count_alleles(typing)
#>    A    B    C DPA1 DPB1 DQA1 DQB1 DRB1 DRB. 
#>    2    2    1    0    0    0    2    2    2 

# Also works with character vectors
typing <- c("A1 A2 B7 B8 Cw3", "Cw3 Cw7", NA)
count_alleles(typing, loci = c("A", "B", "C"))
#> [[1]]
#> A B C 
#> 2 2 1 
#> 
#> [[2]]
#> A B C 
#> 0 0 2 
#> 
#> [[3]]
#>  A  B  C 
#> NA NA NA 
#>