getParticipants: Participants related queries

In reactome/ReactomeContentService4R: Interface for the Reactome Content Service

Participants related queries

Description

Data in Reactome are organized in a hierarchical manner - Pathways contain Reactions, Reactions contain PhysicalEntities. This function is to get the participants of a given Event.

Usage

getParticipants(
  event.id,
  retrieval = c("AllInstances", "PhysicalEntities", "ReferenceEntities",
    "EventsInPathways")
)

Arguments

event.id	a stable or db id of an Event (pathways and reactions)
retrieval	participants to be retrieved, including "AllInstances", "PhysicalEntities", "ReferenceEntities", "EventsInPathways"

Details

Details on options of retrieval arg:

• AllInstances: retrieves all participants (PhysicalEntities) from a given Event and their ReferenceEntities

• PhysicalEntities: retrieves all the PhysicalEntities that take part in a given Event

• ReferenceEntities: retrieves the ReferenceEntities for all PhysicalEntities in every constituent Pathway/Reaction

• EventsInPathways: recursively retrieves all the Events contained in any given Event

Value

a dataframe containing requested participants

See Also

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

Examples

getParticipants("R-HSA-6804741", "AllInstances")
getParticipants("R-HSA-69306", "EventsInPathways")

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