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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.
Install {gwasrapidd} from CRAN:
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_sizeFind 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 a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.
This work would have not been possible without the precious help from the GWAS Catalog team, particularly Daniel Suveges.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.