immunogenetr (version 0.3.0)

HLA_truncate: HLA_truncate

Description

This function truncates HLA typing values in molecular nomenclature (for example from 4 fields to 2 fields). The truncation is based on the number of fields specified and optionally retains any WHO-recognized suffixes (L, S, C, A, Q, or N) or G and P group designations (G or P). This function will work on individual alleles (e.g. "HLA-A*02:01:01:01") or on all alleles in a GL string (e.g. "HLA-A*02:01:01:01+HLA-A*68:01:01^HLA-DRB1*01:01:01+HLA-DRB1*03:01:01").

Usage

HLA_truncate(
  data,
  fields = 2,
  keep_suffix = TRUE,
  keep_G_P_group = FALSE,
  remove_duplicates = FALSE
)

Value

A string with the HLA typing truncated according to the specified number of fields and optional suffix retention.

Arguments

data

A string containing an HLA allele or a GL string.

fields

An integer specifying the number of fields to retain in the truncated values. Default is 2.

keep_suffix

A logical value indicating whether to retain any WHO-recognized suffixes. Default is TRUE.

keep_G_P_group

A logical value indicating whether to retain any G or P group designations. Default is FALSE.

remove_duplicates

A logical value indicating whether to remove duplicated values from a GL string after truncation. Default is FALSE.

Examples

# The Haplotype_frequencies dataset contains a table with HLA typing spread across multiple columns:
print(Haplotype_frequencies)

# The `HLA_truncate` function can be used to truncate the typing results to 2 fields:
library(dplyr)
Haplotype_frequencies %>% mutate(
  across(
    "HLA-A":"HLA-DPB1",
    ~ HLA_truncate(
      .,
      fields = 2,
      keep_suffix = TRUE,
      keep_G_P_group = FALSE
    )
  )
)