Introduction to Genomewide Association Studies

An introductory workshop to GWAS analysis using PLINK and R

In this workshop we will explore the basics of performing Genomewide Association Studies (GWAS) using a combination of the software plink (http://pngu.mgh.harvard.edu/~purcell/plink/) and R (http://www.r-project.org/).

At a later stage (a separate workshop) we will also introduce the GenABEL package which offers additional functionality of genomic association analyses in R.

This workshop is written to be accessible to a range of people, from those that have never performed any command-line work, to those that just want a refresher. As such I have written it to include clear and straight forward outlines of all R and plink operations, most of the time stepping through these one line at at time.

Workshop manual and files

The workshop manual is available in the form of the GWAS_workshop.pdf file from my GitHub, here is the repository. This contains all the information and code to run through the entire workshop, as well as hopefully helpful information.

Set up

  1. Either clone into this repository or download via the Download ZIP button to the right (on GitHub), then start R and ensure this repository is set as your working directory.
  2. In R run the following: source('scripts/GWAS_workshop_setup.R'). The GWAS_workshop_setup.R script is provided to automatically:
    • extract the example data to example/
    • download OS specific version of plink
    • extract plink binary to bin/
  3. Once you have performed the above you should be able to follow along with the workshop manual.