HLA data

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "README-"
)
library(hlatools)

hlatools

Overview

hlatools provides a collection of tools to work with IPD-IMGT/HLA data

Installation

Install from GitHub using remotes:

remotes::install_github("gschofl/hlatools")

Usage

Get HLA data

clone_IMGTHLA(): Clone the ANHIG/IMGTHLA repo on GitHub to a location specified by the option hlatools.local_repos. Defaults to ~/local/db/.
pull_IMGTHLA(): Send a pull request to ANHIG/IMGTHLA.
check_IMGTHLA(): Check if your local repository is up-to-date.

Read HLA data

A HLA gene can be read into a HLAGene object:

x <- hlatools::HLAGene("DPB1")
x

A number of accessor functions can be used to work with these objects:

x <- hlatools::HLAGene("DPA1")
hlatools::db_version(x)
hlatools::locusname(x)
x1 <- x[hlatools::is_complete(x)][1:10]
hlatools::allele_name(x1)
hlatools::cwd_status(x1)
hlatools::ethnicity(x1)
hlatools::g_group(x1)
hlatools::p_group(x1)
hlatools::sequences(x1)
hlatools::exon(x1, exon = 2)

We can access previous releases of the IPD-IMGT/HLA database:

x <- hlatools::HLAGene("DPB1", db_version = "3.25.0")
x
hlatools::db_version(x)
hlatools::locusname(x)
x[hlatools::cwd_status(x) == "Common"][1:10]

These objects come with an additional set of R6-methods that implement an API used mostly in conjunction with the DR2S package:

x$get_closest_complete_neighbor(allele, partially = TRUE): Find the closest full-length allele based on the genetic distance between exon sequences.
x$get_reference_sequence(allele): Return a BStringSet object of a full-length reference sequence for allele. If allele is not fully known the missing stretches are taken from the allele returned by a call to get_closest_complete_neighbor().