CalEpletMHCII: Calculate class II HLA eplet mismatch.

In hlaR: Tools for HLA Data

Calculate class II HLA eplet mismatch.

Description

Use high resolution HLA(Human Leukocyte Antigen) class II data to calculate class II eplet mismatch for a population of donors and recipients. Mismatch is calculated using logic from 'HLAMatchMaker', developed by Rene Dusquesnoy. Current reference tables supported are 'HLAMatchMaker' v2 and v3. Note: interlocus info only available in v3 reference tables.

Usage

CalEpletMHCII(dat_in, ver = 2)

Arguments

dat_in	A dataframe of recipient and donor's high resolution MHC II data. Each recipient and donor pair are linked by are the “pair_id” column and differentiated by the “subject_type” column.
ver	Version number of HLAMatchMaker based eplet reference table to use.

Value

A list of data tables. - 'single_detail': single molecule class II MHC eplet mismatch table, including mismatched eplet names and the count of eplets mismatched at each allele. - 'overall_count': original input data appended with total count of mismatched eplets. - 'dqdr_risk': DR DQ risk score.

Examples

dat <- read.csv(system.file("extdata/example","MHC_II_test.csv",package="hlaR"),sep=",",header=TRUE)
re <- CalEpletMHCII(dat, ver = 2)

hlaR documentation built on Feb. 16, 2023, 7:04 p.m.