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gwasrapidd

R build status Codecov test coverage License: MIT lifecycle

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 studies related to triple-negative breast cancer:

library(gwasrapidd)
studies <- get_studies(efo_trait = 'triple-negative breast cancer')
studies@studies[1:4]
## # A tibble: 2 x 4
##   study_id  reported_trait         initial_sample_size     replication_sample_s…
##   <chr>     <chr>                  <chr>                   <chr>                
## 1 GCST0023… Breast cancer (estrog… 1,529 European ancestr… 2,148 European ances…
## 2 GCST0101… Breast cancer (estrog… 8,602 European ancestr… <NA>

Find associated variants with study GCST002305:

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.

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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.

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