ramiromagno / Gwasrapidd
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gwasrapidd: an R package to query, download and wrangle GWAS Catalog data
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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
You can install the current version of gwasrapidd with:
# install.packages("remotes")
remotes::install_github("ramiromagno/gwasrapidd")
Cheatsheet
Example
Get the study related to triple-negative breast cancer:
library(gwasrapidd)
studies <- get_studies(efo_trait = 'triple-negative breast cancer')
studies@studies[1:4]
## # A tibble: 1 x 4
## study_id reported_trait initial_sample_size replication_sample_si…
## <chr> <chr> <chr> <chr>
## 1 GCST0023… Breast cancer (estrog… 1,529 European ancest… 2,148 European ancest…
Find associated variants:
variants <- get_variants(study_id = 'GCST002305')
variants@variants[c('variant_id', 'functional_class')]
## # A tibble: 5 x 2
## variant_id functional_class
## <chr> <chr>
## 1 rs4245739 3_prime_UTR_variant
## 2 rs2363956 missense_variant
## 3 rs10069690 intron_variant
## 4 rs3757318 intron_variant
## 5 rs10771399 intergenic_variant
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')
##
## To cite gwasrapidd in publications use:
##
## Ramiro Magno, Ana-Teresa Maia, gwasrapidd: an R package to query,
## download and wrangle GWAS Catalog data, Bioinformatics, btz605, 2
## August 2019, Pages 1-2, https://doi.org/10.1093/bioinformatics/btz605
##
## A BibTeX entry for LaTeX users is
##
## @Article{,
## title = {gwasrapidd: an R package to query, download and wrangle GWAS Catalog data},
## author = {Ramiro Magno and Ana-Teresa Maia},
## journal = {Bioinformatics},
## year = {2019},
## pages = {1--2},
## url = {https://doi.org/10.1093/bioinformatics/btz605},
## }
Contributors
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.
We also thank Hadley’s team for all the brilliant software that has influenced so profoundly the development of this package.
Note that the project description data, including the texts, logos, images, and/or trademarks,
for each open source project belongs to its rightful owner.
If you wish to add or remove any projects, please contact us at [email protected].