HLA_truncate {immunogenetr} | R Documentation |
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
)
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. |
Value
A string with the HLA typing truncated according to the specified number of fields and optional suffix retention.
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
)
)
)