immunogenetr (version 0.3.1)

HLA_mismatch_base: HLA_mismatch_base

Description

A function to return a string of mismatches between recipient and donor HLA genotypes represented as GL strings. The function finds mismatches based on the direction of comparison specified in the inputs and also handles homozygosity. As the name implies, this function is the base for all other mismatch (and matching) functions. This function is not meant to be called directly; it is better to use one of the derivative functions.

Usage

HLA_mismatch_base(
  GL_string_recip,
  GL_string_donor,
  loci,
  direction,
  homozygous_count = 2
)

Value

A character vector, where each element is a string summarizing the mismatches for the specified loci. The strings are formatted as comma-separated locus mismatch entries if multiple loci are supplied, or simple GL strings if a single locus is supplied.

Arguments

GL_string_recip

A GL string representing the recipient's HLA genotype.

GL_string_donor

A GL string representing the donor's HLA genotype.

loci

A character vector specifying the loci to be considered for mismatch calculation. HLA-DRB3/4/5 (and their serologic equivalents DR51/52/53) are considered once locus for this function, and should be called in this argument as "HLA-DRB3/4/5" or "HLA-DR51/52/53", respectively.

direction

A character string indicating the direction of mismatch. Options are "HvG" (host vs. graft) or "GvH" (graft vs. host).

homozygous_count

An integer specifying how to handle homozygosity. Defaults to 2, where homozygous alleles are treated as duplicated for mismatch calculations. Can be specified to be 1, in which case homozygous alleles are treated as single occurrences without duplication.

Examples

file <- HLA_typing_1[, -1]
GL_string <- HLA_columns_to_GLstring(file, HLA_typing_columns = everything())

GL_string_recip <- GL_string[1]
GL_string_donor <- GL_string[2]

loci <- c("HLA-A", "HLA-DRB3/4/5", "HLA-DPB1")
mismatches <- HLA_mismatch_base(GL_string_recip, GL_string_donor, loci, direction = "HvG")
print(mismatches)