open_in_gwas_catalog: Browse GWAS Catalog entities from the GWAS Web Graphical User...

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

Browse GWAS Catalog entities from the GWAS Web Graphical User Interface

Description

This function launches the web browser and opens a tab for each identifier on the GWAS web graphical user interface: https://www.ebi.ac.uk/gwas.

Usage

open_in_gwas_catalog(
  identifier,
  gwas_catalog_entity = c("study", "variant", "trait", "gene", "region", "publication")
)

Arguments

identifier	A vector of identifiers. The identifiers can be: study accession identifiers, variant identifiers, EFO trait identifiers, gene symbol names, cytogenetic regions, or PubMed identifiers.
gwas_catalog_entity	Either 'study' (default), 'variant', 'trait', 'gene', 'region' or 'publication', a scalar character. This argument indicates the type of the identifiers passed in identifier.

Value

Returns TRUE if successful, or FALSE otherwise. But note that this function is run for its side effect.

Examples

# Open studies in GWAS Web Graphical User Interface
open_in_gwas_catalog(c('GCST000016', 'GCST001115'))

# Open variants
open_in_gwas_catalog(c('rs146992477', 'rs56261590'),
  gwas_catalog_entity = 'variant')

# Open EFO traits
open_in_gwas_catalog(c('EFO_0004884', 'EFO_0004343'),
  gwas_catalog_entity = 'trait')

# Open genes
open_in_gwas_catalog(c('DPP6', 'MCCC2'),
  gwas_catalog_entity = 'gene')

# Open cytogenetic regions
open_in_gwas_catalog(c('2q37.1', '1p36.11'),
  gwas_catalog_entity = 'region')

# Open publications
open_in_gwas_catalog(c('25533513', '24376627'),
  gwas_catalog_entity = 'publication')

ramiromagno/gwasrapidd documentation built on Jan. 3, 2024, 10:21 p.m.