GWASapi - R package to connect to the NHGRI-EBI GWAS Catalog of Summary Statistics
See the API documentation as well as Pjotr Prins's documentation at github.
You can install GWASapi from GitHub.
You first need to install the devtools.
install.packages("devtools")
Then use devtools::install_github()
to install GWASapi.
library(devtools)
install_github("rqtl/GWASapi")
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 chromosomeslist_studies()
- List of studieslist_traits()
- List of traitsinfo_study()
- Metadata about a particular studyget_variant()
- Get data frame of associations for a particular variantget_asso()
- Get associations for a particular chromosome regionget_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 1 sec; it can be
controlled with the option GWASapi_delay
. For example, to make the
delay 0.5 seconds, use:
options(GWASapi_delay=0.5)
GWASapi is released under the MIT license.