Package: gwasrapidd 0.99.17

gwasrapidd: 'REST' 'API' Client for the 'NHGRI'-'EBI' 'GWAS' Catalog

'GWAS' R 'API' Data Download. This package provides easy access to the 'NHGRI'-'EBI' 'GWAS' Catalog data by accessing the 'REST' 'API' <https://www.ebi.ac.uk/gwas/rest/docs/api/>.

Authors:Ramiro Magno [aut, cre], Ana-Teresa Maia [aut], CINTESIS [cph, fnd], Pattern Institute [cph, fnd]

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gwasrapidd/json (API)
NEWS

# Install 'gwasrapidd' in R:

install.packages('gwasrapidd', repos = c('https://ramiromagno.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ramiromagno/gwasrapidd/issues

Datasets:

associations_ex01 - Gwasrapidd entities' examples
associations_ex02 - Gwasrapidd entities' examples
cytogenetic_bands - GRCh38 human cytogenetic bands.
studies_ex01 - Gwasrapidd entities' examples
studies_ex02 - Gwasrapidd entities' examples
traits_ex01 - Gwasrapidd entities' examples
traits_ex02 - Gwasrapidd entities' examples
variants_ex01 - Gwasrapidd entities' examples
variants_ex02 - Gwasrapidd entities' examples

On CRAN:

thirdpartyclient biomedicalinformatics genomewideassociation snp association-studies gwas-catalog human rest-client trait trait-ontology

8.34 score 91 stars 2 packages 45 scripts 577 downloads 2 mentions 32 exports 57 dependencies

Last updated 11 months agofrom:88a4fca10e. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 09 2024
R-4.5-win	OK	Nov 09 2024
R-4.5-linux	OK	Nov 09 2024
R-4.4-win	OK	Nov 09 2024
R-4.4-mac	OK	Nov 09 2024
R-4.3-win	OK	Nov 09 2024
R-4.3-mac	OK	Nov 09 2024

Exports:%>%association_to_study association_to_trait association_to_variant bind exists_variant get_associations get_child_efo get_metadata get_studies get_traits get_variants intersect is_ebi_reachable n open_in_dbsnp open_in_gtex open_in_gwas_catalog open_in_pubmed setdiff setequal study_to_association study_to_trait study_to_variant trait_to_association trait_to_study trait_to_variant union variant_to_association variant_to_study variant_to_trait write_xlsx

Dependencies:askpass assertthat brio callr cli concatenate cpp11 crayon curl desc diffobj digest dplyr evaluate fansi fs generics glue hms httr jsonlite lifecycle lubridate magrittr mime openssl pillar pingr pkgbuild pkgconfig pkgload plyr praise prettyunits processx progress ps purrr R6 Rcpp rlang rprojroot stringi stringr sys testthat tibble tidyr tidyselect timechange triebeard urltools utf8 vctrs waldo withr writexl

Frequently asked questions

Rendered fromfaq.Rmdusingknitr::rmarkdownon Nov 09 2024.

Last update: 2022-12-23
Started: 2019-04-13

Getting started with gwasrapidd

Rendered fromgwasrapidd.Rmdusingknitr::rmarkdownon Nov 09 2024.

Last update: 2023-06-04
Started: 2019-04-13

Variants associated with Body Mass Index (BMI)

Rendered frombmi_variants.Rmdusingknitr::rmarkdownon Nov 09 2024.

Last update: 2022-12-23
Started: 2020-07-22

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Pipe operator	%>%
Map an association id to a study id	association_to_study
Map an association id to an EFO trait id	association_to_trait
Map an association id to a variant id	association_to_variant
An S4 class to represent a set of GWAS Catalog associations	associations-class
Bind GWAS Catalog objects	bind
GRCh38 human cytogenetic bands.	cytogenetic_bands
Check if a variant exists in the Catalog.	exists_variant
gwasrapidd entities' examples	associations_ex01 associations_ex02 gc_examples studies_ex01 studies_ex02 traits_ex01 traits_ex02 variants_ex01 variants_ex02
Get GWAS Catalog associations	get_associations
Get all child terms of this trait in the EFO hierarchy	get_child_efo
Get GWAS Catalog metadata	get_metadata
Get GWAS Catalog studies	get_studies
Get GWAS Catalog EFO traits	get_traits
Get GWAS Catalog variants	get_variants
Is the GWAS Catalog REST API server reachable?	is_ebi_reachable
Number of GWAS Catalog entities	n n,associations-method n,studies-method n,traits-method n,variants-method
Browse dbSNP from SNP identifiers.	open_in_dbsnp
Browse GTEx from SNP identifiers.	open_in_gtex
Browse GWAS Catalog entities from the GWAS Web Graphical User Interface	open_in_gwas_catalog
Browse PubMed from PubMed identifiers.	open_in_pubmed
Set operations on GWAS Catalog objects.	intersect setdiff setequal setop union
An S4 class to represent a set of GWAS Catalog studies	studies-class
Map a study id to an association id	study_to_association
Map a study id to a EFO trait id	study_to_trait
Map a study id to a variant id	study_to_variant
Subset an associations object	subset-associations [,associations,character,missing,missing-method [,associations,missing,missing,missing-method [,associations,numeric,missing,missing-method
Subset a studies object	subset-studies [,studies,character,missing,missing-method [,studies,missing,missing,missing-method [,studies,numeric,missing,missing-method
Subset a traits object	subset-traits [,traits,character,missing,missing-method [,traits,missing,missing,missing-method [,traits,numeric,missing,missing-method
Subset a variants object	subset-variants [,variants,character,missing,missing-method [,variants,missing,missing,missing-method [,variants,numeric,missing,missing-method
Map an EFO trait id to an association id	trait_to_association
Map an EFO trait id to a study id	trait_to_study
Map an EFO trait id to a variant id	trait_to_variant
An S4 class to represent a set of GWAS Catalog EFO traits.	traits-class
Map a variant id to an association id	variant_to_association
Map a variant id to a study id	variant_to_study
Map a variant id to an EFO trait	variant_to_trait
An S4 class to represent a set of GWAS Catalog variants	variants-class
Export a GWAS Catalog object to xlsx	write_xlsx