quincunx (version 0.1.9)

get_sample_sets: Get PGS Catalog Sample Sets

Description

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

Value

A sample_sets object.

Arguments

pss_id

A character vector of PGS Catalog sample sets accession identifiers.

pgs_id

A character vector of PGS Catalog score accession identifiers.

set_operation

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

interactive

A logical. If all sample sets 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 indicating download progress from the REST API server.

Details

Please note that all search criteria are vectorised, thus allowing for batch mode search.

Examples

if (FALSE) {
# Search by PGS identifier
get_sample_sets(pgs_id = 'PGS000013')

# Search by the PSS identifier
get_sample_sets(pss_id = 'PSS000068')
}