/lit_manuscript

Primary LanguageR

This repository contains code to reproduce the results in

Bass AJ, Bian S, Wingo AP, Wingo TS, Culter DJ, Epstein MP. Identifying latent genetic interactions in genome-wide association studies using multiple traits. Submitted; 2023.

Overview of directories:

  • simulations/:
    • 00-functions.R: contains functions to simulate genotypes and traits.
    • 01-lit-null.R: type I error rate simulations.
    • 02-lit-alt.R: power simulations.
    • 03-lit-time.R: total computational time.
    • 04-PC.R: testing the principal components of the SQ/CP matrix.
    • 05-figures.R: code to create figures.
  • analysis/:
    • 01-preprocessing.R: preprocessing of the UK Biobank data.
    • 02-run-plink.sh: run PLINK to filter SNPs and individuals from the UK Biobank data. Note that we split the PLINK files into chunks using code from here to distribute across cores.
    • 03-run-lit.R: run LIT on the PLINK files generated from 02-run-plink.sh.
    • 04-run-marginal.R: run Marginal (SQ/CP) and Marginal (SQ) on the PLINK files generated from 02-run-plink.sh.
    • 05-run-gamut.R: run GAMuT on the PLINK files generated from 02-run-plink.sh.
    • UKB_analysis.R: code to analyze results.