immunogenetr (version 0.3.0)

HLA_mismatch_number: HLA_mismatch_number

Description

Calculates the number of mismatched HLA alleles between a recipient and a donor across specified loci. Supports mismatch calculations for host-vs-graft (HvG), graft-vs-host (GvH), or bidirectional.

Usage

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

Value

An integer value or a character string: - If `loci` includes only one locus, the function returns an integer mismatch count for that locus. - If `loci` includes multiple loci, the function returns a character string in the format "Locus1=Count1, Locus2=Count2, ...".

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), "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 count homozygous mismatches. Defaults to 2, where homozygous mismatches are treated as two mismatches, regardless if one or two alleles are supplied in the GL string (in cases where one allele is supplied, it is duplicated by the function). If specified as 1, homozygous mismatches are only counted once, regardless of whether one or two alleles are supplied in the GL string (in cases where two alleles are supplied, the second identical allele is deleted).

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")

# Calculate mismatch numbers (Host vs. Graft)
HLA_mismatch_number(GL_string_recip, GL_string_donor, loci, direction = "HvG")

# Calculate mismatch numbers (Graft vs. Host)
HLA_mismatch_number(GL_string_recip, GL_string_donor, loci, direction = "GvH")

# Calculate mismatch numbers (Bidirectional)
HLA_mismatch_number(GL_string_recip, GL_string_donor,
  loci,
  direction = "bidirectional"
)