Movatterモバイル変換

[0]ホーム
URL:

Skip to content

Navigation Menu

Sign in
Appearance settings

Search code, repositories, users, issues, pull requests...

Provide feedback

We read every piece of feedback, and take your input very seriously.

Saved searches

Use saved searches to filter your results more quickly

 Sign up
Appearance settings

gwasrapidd: an R package to query, download and wrangle GWAS Catalog data

License

Unknown, MIT licenses found

Licenses found

Unknown
LICENSE
MIT
LICENSE.md
NotificationsYou must be signed in to change notification settings

ramiromagno/gwasrapidd

CRAN statusR-CMD-checkLicense: MIT

The goal of{gwasrapidd} is to provide programmatic access to theNHGRI-EBI Catalog of published genome-wideassociation studies.

Get started by reading thedocumentation.

Installation

Install{gwasrapidd} from CRAN:

install.packages("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: 12 × 4##    study_id     reported_trait        initial_sample_size replication_sample_s…¹##    <chr>        <chr>                 <chr>               <chr>##  1 GCST002305   Breast cancer (estro… 1,529 European anc… 2,148 European ancest…##  2 GCST90029052 15-year breast cance… 5,631 European anc… <NA>##  3 GCST90296722 Breast cancer (estro… 2,860 African or A… <NA>##  4 GCST90446470 Breast cancer subtyp… 16,499 European an… <NA>##  5 GCST90446471 Breast cancer subtyp… 16,499 European an… <NA>##  6 GCST90446472 Breast cancer subtyp… 16,499 European an… <NA>##  7 GCST90446474 Breast cancer subtyp… 16,499 European an… <NA>##  8 GCST010100   Breast cancer (tripl… 18,016 European an… <NA>##  9 GCST90454344 Breast cancer (tripl… ~14,900 European a… <NA>## 10 GCST90551896 Triple-negative brea… 262 Bantu-speaking… <NA>## 11 GCST90551897 Triple-negative brea… 262 Bantu-speaking… <NA>## 12 GCST90551898 Triple-negative brea… 262 Bantu-speaking… <NA>## # ℹ abbreviated name: ¹​replication_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

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},##   }

Code of Conduct

Please note that the{gwasrapidd} project is released with aContributor Code ofConduct. Bycontributing to this project, you agree to abide by its terms.

Similar projects

Acknowledgements

This work would have not been possible without the precious help fromthe GWAS Catalog team, particularlyDanielSuveges.

About

gwasrapidd: an R package to query, download and wrangle GWAS Catalog data

Topics

Resources

License

Unknown, MIT licenses found

Licenses found

Unknown
LICENSE
MIT
LICENSE.md

Code of conduct

Contributing

Stars

Watchers

Forks

Packages

No packages published

Contributors5

Languages

[8]ページ先頭
©2009-2025 Movatter.jp