quincunx (version 0.1.7)

get_publications: Get PGS Catalog Publications

Description

Retrieves PGS publications via the PGS Catalog REST API. The REST API is queried multiple times with the criteria passed as arguments (see below). By default all publications 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 associations that match simultaneously all criteria provided, then set set_operation to 'intersection'.

Usage

get_publications(
  pgp_id = NULL,
  pgs_id = NULL,
  pubmed_id = NULL,
  author = NULL,
  set_operation = "union",
  interactive = TRUE,
  verbose = FALSE,
  warnings = TRUE,
  progress_bar = TRUE
)

Value

A publications object.

Arguments

pgp_id

A character vector of PGS Catalog publication accession identifiers.

pgs_id

A character vector of PGS Catalog score accession identifiers.

pubmed_id

An integer vector of PubMed identifiers.

author

A character vector of author names, any author in the list of authors in a publication, .e.g. 'Mavaddat'.

set_operation

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

interactive

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

verbose

A logical indicating whether the function should be verbose about the different queries or not.

warnings

A logical indicating whether to print warnings, if any.

progress_bar

Whether to show a progress bar as the queries are performed.

Details

Please note that all search criteria are vectorised, thus allowing for batch mode search. For more details see the help vignette: vignette("getting-pgs-publications", package = "quincunx").

Examples

if (FALSE) {
# Get PGS publications by their identifier
get_publications(pgp_id = c('PGP000001', 'PGP000002'))

# By polygenic score identifier
get_publications(pgs_id = 'PGS000003')

# By PubMed identifier
get_publications(pubmed_id = '30554720')

# By author's last name
get_publications(author = 'Natarajan')
}