gwasrapidd (version 0.99.17)

get_studies: Get GWAS Catalog studies

Description

Retrieves studies via the NHGRI-EBI GWAS Catalog REST API. The REST API is queried multiple times with the criteria passed as arguments (see below). By default all studies that match the criteria supplied in the arguments are retrieved: this corresponds to the default option set_operation set to 'union'. If you rather have only the studies that match simultaneously all criteria provided, then set set_operation to 'intersection'.

Usage

get_studies(
  study_id = NULL,
  association_id = NULL,
  variant_id = NULL,
  efo_id = NULL,
  pubmed_id = NULL,
  user_requested = NULL,
  full_pvalue_set = NULL,
  efo_uri = NULL,
  efo_trait = NULL,
  reported_trait = NULL,
  set_operation = "union",
  interactive = TRUE,
  verbose = FALSE,
  warnings = TRUE
)

Value

A studies object.

Arguments

study_id

A character vector of GWAS Catalog study accession identifiers.

association_id

A character vector of GWAS Catalog association identifiers.

variant_id

A character vector of GWAS Catalog variant identifiers.

efo_id

A character vector of EFO identifiers.

pubmed_id

An integer vector of PubMed identifiers.

user_requested

A logical (scalar!) indicating to retrieve either studies requested by users of the Catalog (TRUE) or otherwise (FALSE).

full_pvalue_set

A logical (scalar!) indicating to retrieve studies with full summary statistics (TRUE) or studies without it (FALSE).

efo_uri

A character vector of EFO URIs.

efo_trait

A character vector of EFO trait descriptions, e.g., 'uric acid measurement'.

reported_trait

A character vector of phenotypic traits as reported by the original authors of the study.

set_operation

Either 'union' or 'intersection'. This tells how studies retrieved by different criteria should be combined: 'union' binds together all results removing duplicates and 'intersection' only keeps same studies found with different criteria.

interactive

A logical. If all studies are requested, whether to ask interactively if we really want to proceed.

verbose

Whether the function should be verbose about the different queries or not.

warnings

Whether to print warnings.

Details

Please note that all search criteria are vectorised, thus allowing for batch mode search, e.g., one can search by multiple variant identifiers at once by passing a vector of identifiers to variant_id.

Examples

if (FALSE) {
# Get a study by its accession identifier
get_studies(study_id = 'GCST001085', warnings = FALSE)

# Get a study by association identifier
get_studies(association_id = '25389945', warnings = FALSE)

# Get studies by variant identifier
get_studies(variant_id = 'rs3798440', warnings = FALSE)

# Get studies by EFO trait identifier
get_studies(efo_id = 'EFO_0005537', warnings = FALSE)
}