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gwasrapidd: an R package to query, download and wrangle GWAS Catalog data
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R Added is_mapped_gene to genomic contexts of variants. Jul 8, 2019
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README.md

gwasrapidd

Travis build status AppVeyor build status codecov 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, experimental 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_…
##   <chr>     <chr>                 <chr>                <chr>               
## 1 GCST0023… Breast cancer (estro… 1,529 European ance… 2,148 European ance…

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

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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