GWASapi - R package to connect to the NHGRI-EBI GWAS Catalog of Summary Statistics

GWASapi is an R package for connecting to the API for the NHGRI-EBI GWAS Catalog of Summary Statistics.

See the API documentation as well as Pjotr Prins's documentation at github.

Installation

install.packages("GWASapi", repos="https://rqtl.r-universe.dev")

Alternatively, install it from GitHub with the remotes package:

#install.packages("remotes")
library(remotes)
install_github("rqtl/GWASapi")

Usage

For an understanding of the NHGRI-EBI GWAS Catalog of Summary Statistics API, see its documentation, as well as Pjotr Prins's documentation at github

The GWASapi package has a set of functions for connecting to the GWAS Catalog:

check_gwasapi() - Check connection.
list_chr() - List chromosomes
list_studies() - List of studies
list_traits() - List of traits
info_study() - Metadata about a particular study
get_variant() - Get data frame of associations for a particular variant
get_asso() - Get associations for a particular chromosome region
get_trait_asso() - Get associations for a particular trait

For examples, see the online vignette, which is also available from within R:

vignette("GWASapi")

Note that we enforce a delay between calls to the API, to slow repeated calls within a loop. The default is 2 sec because we were getting a lot of "too many requests" errors. It can be controlled with the option GWASapi_delay. For example, to make the delay 2 seconds, use:

options(GWASapi_delay=2)

License

GWASapi is released under the MIT license.