immunogenetr (version 0.3.0)

HLA_validate: HLA_validate

Description

Returns only HLA alleles in valid nomenclature, either serologic or molecular. Simple numbers, such as "2" or "27" will be returned as-is. Suffixes that are not WHO-recognized suffixes (L, S, C, A, Q, N) or G or P group designations will be removed. For example "novel" at the end of the allele will be removed, while "n" at the end of the allele will be retained. Other values, such as "blank" or "-" will be converted to NA values. This function is helpful for cleaning up the typing of an entire table of HLA values.

Usage

HLA_validate(data)

Value

A string with a valid HLA allele or NA if no valid allele was present.

Arguments

data

A string containing an HLA allele.

Examples

HLA_validate("HLA-A2")
HLA_validate("A*02:01:01:01N")
HLA_validate("A*02:01:01N")
HLA_validate("HLA-DRB1*02:03novel")
HLA_validate("HLA-DQB1*03:01v")
HLA_validate("HLA-DRB1*02:03P")
HLA_validate("HLA-DPB1*04:01:01G")
HLA_validate("2")
HLA_validate(2)
HLA_validate("B27")
HLA_validate("A*010101")
HLA_validate("-")
HLA_validate("blank")

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

# Cleaning up the entire table. Note that blank values will be converted to "NA".
library(dplyr)
HLA_typing_LIS %>% mutate(
  across(
    mA1Cd.recipient:mDPB12cd.recipient,
    ~ HLA_validate(.)
  )
)