The OpenGWAS database comprises over 50,000 curated, QC’d and harmonised complete GWAS summary datasets and can be queried using an API. See here for documentation on the API itself. This R package is a wrapper to make generic calls to the API, plus convenience functions for specific queries.
Methods currently implemented:
- Get meta data about specific or all studies
- Obtain the top hits (with on the fly clumping as an option) from each of the GWAS datasets. Clumping and significance thresholds can be specified
- Obtain the summary results of specific variants across specific studies. LD-proxy lookups are performed automatically if a specific variant is absent from a study
- Query a genomic region in a GWAS dataset, e.g. for fine mapping or colocalisation analysis
- Perform PheWAS
There are a few convenience functions also:
- Query dbSNP data, allowing conversion between chromosome:position and rsids and getting annotations
- Perform LD clumping using the server, or locally
- Obtain LD matrices for a list of SNPs using the server or locally (e.g. for fine mapping, colocalisation or Mendelian randomization)
See https://github.com/MRCIEU/gwasglue2 for information about how to connect the genotype and LD data to other packages involving colocalisation, finemapping, visualisation and MR.
Installation
Install from CRAN using:
install.packages("ieugwasr")or install the developer version of ieugwasr with:
remotes::install_github("mrcieu/ieugwasr")Browse the vignettes etc for information on how to use this package: https://mrcieu.github.io/ieugwasr/