quincunx (version 0.1.9)

get_traits: Get PGS Catalog Traits

Description

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

Usage

get_traits(
  efo_id = NULL,
  trait_term = NULL,
  exact_term = TRUE,
  include_children = FALSE,
  set_operation = "union",
  interactive = TRUE,
  verbose = FALSE,
  warnings = TRUE,
  progress_bar = TRUE
)

Value

A traits object.

Arguments

efo_id

A character vector of EFO identifiers.

trait_term

A character vector of terms to be matched against trait identifiers (efo_id), trait descriptions, synonyms thereof, externally mapped terms, or even trait categories.

exact_term

A logical value, indicating whether to match the trait_term exactly (TRUE) or not (FALSE).

include_children

A logical value, indicating whether to include child traits or not.

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 traits 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) {
# Get a trait by its EFO identifier
get_traits(efo_id = 'EFO_0004631')

# Get a trait by matching a term in EFO identifier (`efo_id`), label,
# description synonyms, categories, or external mapped terms
get_traits(trait_term = 'stroke', exact_term = FALSE)

# Get a trait matching its name (`trait`) exactly (default)
get_traits(trait_term = 'stroke', exact_term = TRUE)

# Get traits, excluding its children traits (default)
get_traits(trait_term = 'breast cancer')

# Get traits, including its children traits (check column `is_child` for
# child traits)
get_traits(trait_term = 'breast cancer', include_children = TRUE)
}