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
)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.
Value
A studies object.
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)
}