HLA_match_number {immunogenetr} | R Documentation |
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"
)
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"). |
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, ...".
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"
)