hla-assoc

This repository houses the scripts that were used to generate data for the paper "Pervasive additive and non-additive effects within the HLA region contribute to disease risk in the UK Biobank". The biorxiv link can be found [here].

Cloning

Clone using git lfs clone git@github.com:rivas-lab/hla-assoc.git. If you don't use LFS to clone, you may need to to do git lfs pull after you clone to pull in the files tracked by LFS.

Git LFS

The files in output directory are tracked with git LFS.

Directories

hla_genotype_data

This directory contains metadata files on UK Biobank genotype data. Note: Actual genotype data (in the form of R data structures, .rds, are on Sherlock but not committed to the GitHub - see .gitignore).

html

This directory contains data needed for visualization of HLA on GBE.

scripts

This directory contains the scripts used to generate the data in the output directory.

output

This directory is tracked by Git LFS and contains data files that were generated by scripts in this repository.

notebooks

This directory contains the notebooks used to generate the figures for the [paper].

figures

Contains the figures of the [paper] generated by the notebooks.