zrchao / gwasglue

Linking GWAS data to analytical tools in R

gwasglue

Under development

This R package serves as a conduit between packages that can read or query GWAS summary data, and packages that can analyse GWAS summary data. Here is where it lies in the general ecosystem of GWAS data and analysis:

The figure above depicts a set of packages that we plan to connect to. Here is a list of what has been done and what is still to do:

Data sources

• ieugwasr
• gwasvcf

Finemapping

• finemapr
• FINEMAP
• PAINTOR
• CAVIAR
• SuSIE - TODO
• JAM - TODO

Colocalisation

• coloc
• HEIDI - TODO
• eCAVIAR - TODO
• S-Predixcan - TODO

Mendelian randomization

• TwoSampleMR
• MendelianRandomization - port from TwoSampleMR
• RadialMR - port from TwoSampleMR
• MRPRESSO - port from TwoSampleMR
• GSMR - TODO
• MRMix - TODO

Visualisation

• gassocplot
• Locus zoom plots e.g. [https://github.com/jrs95/gassocplot] - TODO

Installation

You can install the development version of gwasglue with:

devtools::install_github("mrcieu/gwasglue")

Usage

See vignettes etc here: https://mrcieu.github.io/gwasglue.

Reference datasets

Example GWAS VCF (GIANT 2010 BMI):

• http://fileserve.mrcieu.ac.uk/vcf/IEU-a-2.vcf.gz
• http://fileserve.mrcieu.ac.uk/vcf/IEU-a-2.vcf.gz.tbi

Updated 1000 genomes LD reference panels (multiple populations):

• http://fileserve.mrcieu.ac.uk/ld/1kg.v3.tgz

1kg European reference panel for LD (legacy):

• http://fileserve.mrcieu.ac.uk/ld/data_maf0.01_rs_ref.tgz

1kg vcf harmonised against human genome reference:

• http://fileserve.mrcieu.ac.uk/vcf/1kg_v3_nomult.vcf.gz
• http://fileserve.mrcieu.ac.uk/vcf/1kg_v3_nomult.vcf.gz.tbi

Contributing to the resource

For any <analysis> package we create a new file called R/<analysis>.r which contains two functions:

• gwasvcf_to_<analysis>
• ieugwasr_to_<analysis>

For an example, see the R/TwoSampleMR.r file, which contains the functions gwasvcf_to_TwoSampleMR and ieugwasr_to_TwoSampleMR.