quincunx (version 0.1.9)

get_scores: Get PGS Catalog Scores

Description

Retrieves polygenic scores via the PGS Catalog REST API. The REST API is queried multiple times with the criteria passed as arguments (see below). By default all scores 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_scores(
  pgs_id = NULL,
  efo_id = NULL,
  pubmed_id = NULL,
  set_operation = "union",
  interactive = TRUE,
  verbose = FALSE,
  warnings = TRUE,
  progress_bar = TRUE
)

Value

A scores object.

Arguments

pgs_id

A character vector of PGS Catalog score accession identifiers.

efo_id

A character vector of EFO identifiers.

pubmed_id

An integer vector of PubMed identifiers.

set_operation

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

interactive

A logical. If all scores 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.

Examples

if (FALSE) {
# By `pgs_id`
get_scores(pgs_id = 'PGS000088')

# By `efo_id`
get_scores(efo_id = 'EFO_0007992')

# By `pubmed_id`
get_scores(pubmed_id = '25748612')
}