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HLA Genotyping in UKB

ukb_hla_typing.Rd

Parse UK Biobank HLA v2 compound field (22182) and derive per-locus genotypes

Usage

ukb_hla_typing(df, header, col = "p22182", q_threshold = 0.7)

Arguments

df

A data.frame/tibble with eid and a compound column (default p22182).

header

Allele column order, e.g. ukb_hla_header() (character vector).

col

Compound column name. Default "p22182".

q_threshold

Posterior threshold (UKB commonly uses 0.7). Default 0.7.

Value

A list with:

  • calls: data.table with per-allele calls (eid, locus, allele, allele_pretty, allele_copies, allele_q).

  • genotype: data.table with per-locus genotype strings (eid, locus, genotype).

Examples

if (FALSE) { # \dontrun{
library(tidyverse)
# x <- data.table::fread("~/Project/UKB/data/HLA.csv")
# x <- data.table::fread("HLA.csv")         # eid + p22182
header <- ukb_hla_header()
res <- ukb_hla_typing(x, header)
res$genotype %>% dplyr::filter(locus == "B") %>% dplyr::slice_head(n = 5)
} # }