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
At a later stage (a separate workshop) we will also introduce the
GenABEL package which offers additional functionality of genomic association analyses in
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.
- Either clone into this repository or download via the
Download ZIPbutton to the right (on GitHub), then start
Rand ensure this repository is set as your working directory.
Rrun 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
plinkbinary to bin/
- Once you have performed the above you should be able to follow along with the workshop manual.