Skip to contents

Translates HLA alleles in v2 notation to v3

Source: R/clean_hla.R
convert_v2_to_v3.Rd

The pre-2010 "v2" notation does not include the field delimiters (:) that are now mandatory in v3. This function first tests if an allele is in v2 format; if an allele is not in v2 format; it's left alone. But if it is, it looks up its v2 equivalent in the v2_to_v3 lookup table. If it is not in the table, a v3 version is put together heuristically, by inserting : after every two digits.

Usage

convert_v2_to_v3(allele)

Arguments

allele

A string or character vector of HLA alleles

Value

A vector with the same length as allele, with all v2 alleles converted to v3

Details

N.B. The heuristic prediction will not work in all cases. For example:

  • DPB1*87801N should be DPB1*878:01N (but is output as DPB1*87:801N)

  • DPB1*152401 should be DPB1*1524:01 (but is output as DPB1*15:24:01)

In general it's not possible to make this work purely syntactically without imbuing knowledge on which HLA alleles exist and which do not. For example, should DRB1*1412601 be 14:126:01 or 14:12:601? Both are theoretically possible. However, alleles with > 2 digits per field are rare, and were not really around before 2010, so in practice one should rarely encounter them in v2 format.

Examples

convert_v2_to_v3("A*01010101") # known v2 allele
#> [1] "A*01:01:01:01"
convert_v2_to_v3("B*0701") # not a known v2 allele, but heuristic works
#> [1] "B*07:01"
convert_v2_to_v3("B*9526") # known allele where heuristic would not work
#> [1] "B*15:126"