immunogenetr (version 0.3.0)

HLA_match_number: HLA_match_number

Description

Calculates the number of HLA matches as two minus the number of mismatches from `HLA_mismatch_number`. Homozygous mismatches are counted twice. Supports match calculations for host-vs-graft (HvG), graft-vs-host (GvH), or bidirectional. Bidirectional matching is the default, but can be overridden using the "direction" argument.

Usage

HLA_match_number(
  GL_string_recip,
  GL_string_donor,
  loci,
  direction = "bidirectional"
)

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 match. Options are "HvG" (host vs. graft), "GvH" (graft vs. host), "bidirectional" (the minimum value of "HvG" and "GvH").

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-B")

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

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

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