gwasrapidd (version 0.99.17)

get_variants: Get GWAS Catalog variants

Description

Retrieves variants 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 variants 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 variants that match simultaneously all criteria provided, then set set_operation to 'intersection'.

Usage

get_variants(
  study_id = NULL,
  association_id = NULL,
  variant_id = NULL,
  efo_id = NULL,
  pubmed_id = NULL,
  genomic_range = NULL,
  cytogenetic_band = NULL,
  gene_name = NULL,
  efo_trait = NULL,
  reported_trait = NULL,
  set_operation = "union",
  interactive = TRUE,
  std_chromosomes_only = TRUE,
  verbose = FALSE,
  warnings = TRUE
)

Value

A variants 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.

genomic_range

A named list of three vectors:

chromosome

A character vector of chromosome names of the form 1--22, X or Y.

start

A numeric vector of start positions, starting at 1.

end

A numeric vector of end positions.

The three vectors need to be of the same length so that chromosome names, start and end positions can be matched by position.

cytogenetic_band

A character vector of cytogenetic bands of the form '1p36.11'.

gene_name

Gene symbol according to HUGO Gene Nomenclature (HGNC).

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 variants retrieved by different criteria should be combined: 'union' binds together all results removing duplicates and 'intersection' only keeps same variants found with different criteria.

interactive

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

std_chromosomes_only

Whether to return only variants mapped to standard chromosomes: 1 thru 22, X, Y, and MT.

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

# Get variants by study identifier
get_variants(study_id = 'GCST001085', warnings = FALSE)

# Get a variant by its identifier
if (FALSE) {
get_variants(variant_id = 'rs3798440', warnings = FALSE)
}