immunogenetr (version 0.3.1)

HLA_mismatched_alleles: HLA_mismatched_alleles

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.

Usage

HLA_mismatched_alleles(
  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 were supplied, or as simple GL strings if a single locus was supplied.

Arguments

GL_string_recip

A GL strings representing the recipient's HLA genotypes.

GL_string_donor

A GL strings representing the donor's HLA genotypes.

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), "GvH" (graft vs. host), "bidirectional" (the max value of "HvG" and "GvH"), or "SOT" (host vs. graft, as is used for mismatching in solid organ transplantation).

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 as 1, in which case homozygous alleles are treated as single occurrences without duplication (in other words, homozygous mismatches are only "counted" once).

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_mismatched_alleles(GL_string_recip, GL_string_donor, loci, direction = "HvG")
print(mismatches)