getEntities: PhysicalEntity queries

In reactome/ReactomeContentService4R: Interface for the Reactome Content Service

PhysicalEntity queries

Description

This method retrieves instances related to PhysicalEntity.

Usage

getEntities(
  id,
  retrieval = c("subunits", "complexes", "componentOf", "otherForms"),
  resource = "Reactome",
  subunitsExcludeStructures = FALSE
)

Arguments

id	stable or db id of a Reactome PhysicalEntity, or id from resources other than Reactome
retrieval	entities to be retrieved, including "subunits", "complexes", "componentOf", "otherForms"
resource	resource other than Reactome, e.g. UniProt, Ensembl
subunitsExcludeStructures	whether contained Complexes and EntitySets are excluded when retrieving "subunits"

Details

Details on options of retrieval arg:

• subunits: retrieves subunits that constitute any given Complex

• complexes: retrieves Complexes that contain the given id and resource

• componentOf: retrieves structures (Complexes and Sets) that include the given Entity as their component

• otherForms: retrieves Entities containing all other forms of the given PhysicalEntity

Value

a dataframe containing requested information

See Also

Other getContent: getEventsHierarchy(), getOrthology(), getParticipants(), getPathways(), getPerson(), getSchemaClass(), getSpecies(), query()

Examples

getEntities("R-HSA-5674003", retrieval="subunits")
getEntities("P00533", retrieval="complexes", resource="UniProt")

reactome/ReactomeContentService4R documentation built on May 1, 2023, 5:33 a.m.