GLstring_drop_non_expressed: GLstring_drop_non_expressed

In immunogenetr: A Comprehensive Toolkit for Clinical HLA Informatics

GLstring_drop_non_expressed

Description

This function removes alleles carrying a WHO expression suffix from a GL String. By default the suffixes N (null), S (secreted) and C (cytoplasmic) are removed, on the reasoning that these alleles do not produce a protein at the cell surface; L (low), Q (questionable) and A (aberrant) alleles are kept, as some surface expression is possible. Which suffixes to treat as non-expressed is a clinical judgement, so the 'suffixes' argument can be set to any combination of the six.

Removal operates on whole alleles at any level of the GL String hierarchy: an allele ambiguity list narrows, a gene copy with no expressed alleles collapses, and a locus with no expressed alleles disappears along with its delimiter. If nothing in a GL String survives, 'NA' is returned for that entry.

Usage

GLstring_drop_non_expressed(GL_string, suffixes = c("N", "S", "C"))

Arguments

GL_string	A character vector of GL Strings.
suffixes	A character vector of WHO expression suffixes to remove. Any combination of "N", "Q", "L", "S", "C" and "A". Defaults to 'c("N", "S", "C")'.

Value

A character vector of GL Strings with the selected alleles removed, the same length as 'GL_string'. Entries with no remaining alleles are 'NA'.

Examples

# A null allele is removed from an allele ambiguity list, and a gene copy
# with no expressed alleles collapses:
GLstring_drop_non_expressed(
  "HLA-A*01:01N+HLA-A*02:01^HLA-B*07:02/HLA-B*07:02N+HLA-B*08:01"
)

# A locus with no expressed alleles disappears along with its delimiter:
GLstring_drop_non_expressed("HLA-A*01:01N+HLA-A*02:01N^HLA-B*07:02+HLA-B*08:01")

# L, Q and A alleles are kept by default; narrow `suffixes` to remove only
# null alleles:
GLstring_drop_non_expressed("HLA-A*24:02Q+HLA-A*01:01")
GLstring_drop_non_expressed("HLA-A*01:01N+HLA-A*30:14L", suffixes = "N")

immunogenetr documentation built on Aug. 20, 2026, 1:07 a.m.