README.md

In rqtl/GWAScat: NHGRI-EBI GWAS Catalog of Summary Statistics

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.

Installation

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")

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 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)

License

GWASapi is released under the MIT license.

rqtl/GWAScat documentation built on Nov. 5, 2019, 4:15 a.m.