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:
- coloc
- HEIDI - TODO
- eCAVIAR - TODO
- S-Predixcan - TODO
- TwoSampleMR
- MendelianRandomization - port from TwoSampleMR
- RadialMR - port from TwoSampleMR
- MRPRESSO - port from TwoSampleMR
- GSMR - TODO
- MRMix - TODO
- gassocplot
- Locus zoom plots e.g. [https://github.com/jrs95/gassocplot] - TODO
You can install the development version of gwasglue with:
devtools::install_github("mrcieu/gwasglue")See vignettes etc here: https://mrcieu.github.io/gwasglue.
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):
1kg European reference panel for LD (legacy):
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
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.