Query the 'OpenGWAS' Genotype-Phenotype Map

Client for the 'OpenGWAS' genotype-phenotype map ('GPMap') API < https://gpmap.opengwas.io>, which brings together colocalisation, rare variant and molecular QTL results across thousands of traits. Functions retrieve traits, genes, variants and genomic regions with their colocalising studies, associations, linkage disequilibrium and pleiotropy summaries, search the map by name or variant, and upload GWAS summary statistics for analysis against it.

gpmapr

gpmapr is an R client for the OpenGWAS Genotype-Phenotype Map. You can:

search the map for traits, genes and variants;
fetch their colocalisation groups, rare-variant results and associations;
upload your own GWAS to compare against the map.

Installation

Install the package from GitHub:

# install.packages("pak")
pak::pak("MRCIEU/gpmapr")

Usage

library(gpmapr)

# Find a trait, gene or variant
search_gpmap("haemoglobin")

# Then fetch it with the call shown in the `call` column
result <- trait(5020)
head(result$coloc_groups)

See vignette("gpmapr") to get started.

Updating

gpmapr checks on the first request of each session that it supports the version of the GPMap API. If the API has changed, you'll see an error asking you to update. Update with: