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Getting setup

In this practical we will run command-line programs to perform the analyses, and R to interpret them. If you haven't installed these already, visit the prerequisites section for a guide.

To get set up, you need

  • the datasets from the practical folder.
  • the command-line programs we'll use

Moving to the right folder​

Before starting please check your terminal is in the right folder. A good choice is your home folder:

cd ~

However if you are using Ubuntu for Windows, you should instead change to your main Desktop folder (this is so that the results work well with RStudio):

cd /mnt/c/Users/<your user name>/Desktop/

Downloading the data​

To get the data, download and extract the tarball from this folder:

curl -O https://www.chg.ox.ac.uk/~gav/projects/chg-training-resources/data/genome_wide_association_studies/genome_wide_association_analysis/gwas_practical.tgz

This might take a minute or two. Once the download has completed, extract the tarball and cd into the newly-created directory:

tar -xzf gwas_practical.tgz
cd gwas_practical

If you explore this directory, you should see there are a number of files and a resources and scripts folder:

$ ls
chr19-example.pca      chr19-example.vcf.gz  resources  snp-example.samples
chr19-example.samples  plink_versions        scripts    snp-example.vcf

Next let's get the plink program we need. There are two ways to get this:

  • The plink_versions/ folder contains Mac OS and Linux versions of the plink executable. To get that, move the appopriate version into this folder:
mv plink_versions/plink_linux/plink ./

or

mv plink_versions/plink_mac/plink ./
Note

If you are using Ubuntu for Windows, the appropriate version is the 'Linux 64 bit' version.

Alternatively, you can download the appropriate version from the plink website. Extract the archive and move the plink executable into this folder.

When all is set up you should now be able to run plink like this:

./plink –-version

Plink will tell you its version, and when it was last updated.

Setting up R​

Make sure your RStudio session is also pointing at the gwas_practical folder (use setwd() or the Session->Set Working Directory menu to do this.