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gwasrapidd: an R package to query, download and wrangle GWAS Catalog data
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The goal of{gwasrapidd} is to provide programmatic access to theNHGRI-EBI Catalog of published genome-wideassociation studies.
Get started by reading thedocumentation.
Install{gwasrapidd} from CRAN:
install.packages("gwasrapidd")
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: 3 × 4## study_id reported_trait initial_sample_size replication_sample_s…¹## <chr> <chr> <chr> <chr>## 1 GCST002305 Breast cancer (estrog… 1,529 European anc… 2,148 European ancest…## 2 GCST010100 Breast cancer (estrog… 8,602 European anc… <NA>## 3 GCST90029052 15-year breast cancer… 5,631 European anc… <NA>## # ℹ abbreviated name: ¹replication_sample_size
Find associated variants with study GCST002305:
variants<- get_variants(study_id='GCST002305')variants@variants[c('variant_id','functional_class')]## # A tibble: 5 × 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
{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},## }
Please note that the{gwasrapidd} project is released with aContributor Code ofConduct. Bycontributing to this project, you agree to abide by its terms.
- Bioconductor R packagegwascat by Vincent J Carey:https://www.bioconductor.org/packages/release/bioc/html/gwascat.html
- Web applicationPhenoScanner V2 by Mihir A. Kamat, James R. Staley,and others:http://www.phenoscanner.medschl.cam.ac.uk/
- Web applicationGWEHS: Genome-Wide Effect sizes and HeritabilityScreener by Eugenio López-Cortegano and Armando Caballero:http://gwehs.uvigo.es/
This work would have not been possible without the precious help fromthe GWAS Catalog team, particularlyDanielSuveges.
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gwasrapidd: an R package to query, download and wrangle GWAS Catalog data