immunogenetr (version 0.3.0)

GLstring_regex: GLstring_regex

Description

This function will format an HLA allele (e.g. "HLA-A*02:01") to a regex pattern for searching within a GL string. Note that in order for this function to work properly, the full HLA allele name, including prefixes, is required. Allele values of "A*02:01" will need to be updated to "HLA-A*02:01", and "A2" will need to be updated to "HLA-A2". The `HLA_prefix_add` function is useful in these situations.

Usage

GLstring_regex(data)

Value

A string with the HLA allele formatted as a regex pattern.

Arguments

data

A string containing an HLA allele.

Examples

# To understand how the function works we can see how it alters the allele "HLA-A*02:01":

GLstring_regex("HLA-A*02:01")

# The result is the same allele with extra formatting to escape special characters found
# in a GL string, as well as the ability to accurately search for an allele in a GL string.
# For example, we would not want the allele "HLA-A*02:14" to match to "HLA-A*02:149:01",
# which would happen if we simply escaped the special characters:

library(stringr)
str_view("HLA-A*02:149:01", str_escape("HLA-A*02:14"), match = NA)

# Using `GLstring_regex` prevents this:

str_view("HLA-A*02:149:01", GLstring_regex("HLA-A*02:14"), match = NA)

# Using a longer GL string with multiple alleles and loci:

GL_string <- "HLA-A*02:01:01+HLA-A*68:01^HLA-B*07:01+HLA-B*15:01"

# We can match any allele accurately:

str_view(GL_string, GLstring_regex("HLA-A*68:01"), match = NA)

# Note that alleles supplied with fewer fields than in the GL string will also match:

str_view(GL_string, GLstring_regex("HLA-A*02:01"), match = NA)