/GWAStutorial

GWAS tutorial

Primary LanguageR

Genome-wide association (GWA) tutorial

Additional files

For this tutorial you will additionally need the files

  • 117Malay_282lipids.txt
  • 120Indian_282lipids.txt
  • 122Chinese_282lipids.txt
  • 105Indian_2527458snps.bed, .bim, .fam
  • 108Malay_2527458snps.bed, .bim, .fam
  • 110Chinese_2527458snps.bed, .bim, .fam

stored in the folders 'Lipidomic' and 'Genomics' contained in the following .gz: http://phg.nus.edu.sg/StatGen/public_html/Iomics/downloads/iOmics_data.tar.gz

Instructions

  1. Combine the folders 'Lipidomic' and 'Genomics' and all files from this repo in your working directory.
  2. Install all packages listed on top of the scripts. snpStats and SNPRelate are deposited in BioConductor, all other packages in CRAN.
  3. Run the scripts in their exact numbered order.

Acknowledgements

This work was largely based on the following publications:

  • Establishing multiple omics baselines for three Southeast Asian populations in the Singapore Integrative Omics Study, Saw et al. (2017), Nat. Comm. (data source)
  • A guide to genome-wide association analysis and post-analytic interrogation, Reed et al. (2015), Stats. in Med. (method source)

Enjoy, any feedback is welcome!

Francisco