In ramiromagno/gwasrapidd: 'REST' 'API' Client for the 'NHGRI'-'EBI' 'GWAS' Catalog

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gwasrapidd

The goal of {gwasrapidd} is to provide programmatic access to the NHGRI-EBI Catalog of published genome-wide association studies.

Get started by reading the documentation.

Installation

Install {gwasrapidd} from CRAN:

install.packages("gwasrapidd")

Cheatsheet

Example

Get studies related to triple-negative breast cancer:

library(gwasrapidd)
studies <- get_studies(efo_trait = 'triple-negative breast cancer')
studies@studies[1:4]

Find associated variants with study r studies@studies$study_id[1]:

variants <- get_variants(study_id = 'GCST002305')
variants@variants[c('variant_id', 'functional_class')]

Citing this work

{gwasrapidd} was published in Bioinformatics in 2019: https://doi.org/10.1093/bioinformatics/btz605.

To generate a citation for this publication from within R:

citation('gwasrapidd')

Code of Conduct

Please note that the {gwasrapidd} project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

Similar projects

• Bioconductor R package gwascat by Vincent J Carey: https://www.bioconductor.org/packages/release/bioc/html/gwascat.html
• Web application PhenoScanner V2 by Mihir A. Kamat, James R. Staley, and others: http://www.phenoscanner.medschl.cam.ac.uk/
• Web application GWEHS: Genome-Wide Effect sizes and Heritability Screener by Eugenio López-Cortegano and Armando Caballero: http://gwehs.uvigo.es/

Acknowledgements

This work would have not been possible without the precious help from the GWAS Catalog team, particularly Daniel Suveges.

ramiromagno/gwasrapidd documentation built on Jan. 3, 2024, 10:21 p.m.