Determine the level of resolution of an HLA-allele

get_resolution() takes in a string or character vector of HLA alleles, and returns their resolution as either low, intermediate, or high.

Usage

get_resolution(allele, extended = FALSE)

Arguments

allele

A string or character vector with (an) HLA allele(s).

extended

When TRUE, the returned resolution also contains:

• for high resolution: the number of fields ("second field", "third field", "fourth field")

• for low resolution: whether the allele is a serological/molecular split/broad or associated antigen

Value

A string or character vector of the same length as allele, with "low", "intermediate", or "high" for each element.

Details

Resolution is defined as follows:

• Low: a typing at the allele group level, such as

  • anything using the serological/antigen nomenclature, e.g A2

  • an XX code representing an allele group, e.g. A*02:XX

• Intermediate: any typing with ambiguities, such as

  • a list using the forward slash notation, e.g. HLA-A*23:26/HLA-A*23:39

  • a typing with multiple allele codes, e.g. A*01:AABJE

• High: any typing with more than 2 field codes, e.g.

  • A*24:09 (minimum)

  • HLA-A*24:02:01:02L (maximum)

Examples

get_resolution("A2") # low
#> [1] "low"
get_resolution("A2", extended = TRUE) # low - broad
#> [1] "serology - broad"
get_resolution("A*01:AABJE") # intermediate
#> [1] "intermediate"
get_resolution("A*24:09") # high
#> [1] "high"
get_resolution("A*24:09", extended = TRUE) # high - second field
#> [1] "high - second field"

# also works with character vectors, or in a data frame
allele_vec <- c("A2", "A*01:AABJE", "B*42:08")
get_resolution(allele_vec)
#> [1] "low"          "intermediate" "high"        

tidyr::tibble(alleles = allele_vec) |>
  dplyr::mutate(resolution = get_resolution(allele_vec))
#> # A tibble: 3 × 2
#>   alleles    resolution  
#>   <chr>      <chr>       
#> 1 A2         low         
#> 2 A*01:AABJE intermediate
#> 3 B*42:08    high