quincunx (version 0.1.7)

get_performance_metrics: Get PGS Catalog Performance Metrics

Description

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

Value

A performance_metrics object.

Arguments

ppm_id

A character vector of PGS Catalog performance metrics 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 performance metrics found with different criteria.

interactive

A logical. If all performance metrics 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) {
# Get performance metrics catalogued with identifier 'PPM000001'
get_performance_metrics(ppm_id = 'PPM000001')

# Get performance metrics associated with polygenic score id 'PGS000001'
get_performance_metrics(pgs_id = 'PGS000001')

# To retrieve all catalogued performed metrics in PGS Catalog you simply
# leave the parameters `ppm_id` and `pgs_id` as `NULL`.
get_performance_metrics()
}