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:
install.packages("gwasrapidd")You can instead install the development version of
{gwasrapidd} by setting Ramiro Magno’s universe
repository:
options(repos = c(ramiromagno = 'https://ramiromagno.r-universe.dev',
CRAN = 'https://cloud.r-project.org'))
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 initi…¹ repli…²
## <chr> <chr> <chr> <chr>
## 1 GCST002305 Breast cancer (estrogen-receptor negative, proge… 1,529 … 2,148 …
## 2 GCST010100 Breast cancer (estrogen-receptor negative, proge… 8,602 … <NA>
## 3 GCST90029052 15-year breast cancer-specific survival (ER nega… 5,631 … <NA>
## # … with abbreviated variable names ¹initial_sample_size,
## # ²replication_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.