event: Reactome Data: Queries related to events

In VonWebEinstein/ReactomeAPI:

Description

The reactomeEvent function can query data to given event, including ancestors, participants, participatingPhysicalEntities, participatingReferenceEntities, given as the argument type.

Usage

reactomeEvent(id, type, silent = FALSE)

rtEvent(id, type, silent = FALSE)

Arguments

id	string. The event for which the ancestors etc. are requested.
type	string. Can be ancestors, participants, participatingPhysicalEntities, or participatingReferenceEntities
silent	logical. Whether print error messages on the screen.

Value

A data frame.

Note

ancestors: The Reactome definition of events includes pathways and reactions. Although events are organised in a hierarchical structure, a single event can be in more than one location, i.e. a reaction can take part in different pathways while, in the same way, a sub-pathway can take part in many pathways. Therefore, this method retrieves a list of all possible paths from the requested event to the top level pathway(s).

participants: Participants contains a PhysicalEntity (dbId, displayName) and a collection of ReferenceEntities (dbId, name, identifier, url)

participatingPhysicalEntities: This method retrieves all the PhysicalEntities that take part in a given event. It is worth mentioning that because a pathway can contain smaller pathways (subpathways), the method also recursively retrieves the PhysicalEntities from every constituent pathway.

participatingReferenceEntities: PhysicalEntity instances that represent, e.g., the same chemical in different compartments, or different post-translationally modified forms of a single protein, share numerous invariant features such as names, molecular structure and links to external databases like UniProt or ChEBI.

To enable storage of this shared information in a single place, and to create an explicit link among all the variant forms of what can also be seen as a single chemical entity, Reactome creates instances of the separate ReferenceEntity class. A ReferenceEntity instance captures the invariant features of a molecule.

This method retrieves the ReferenceEntities of all PhysicalEntities that take part in a given event. It is worth mentioning that because a pathway can contain smaller pathways (subpathways), this method also recursively retrieves the ReferenceEntities for all PhysicalEntities in every constituent pathway.

See Also

reactomeEventHierarchy

Examples

# The ancestors of a given event
res = reactomeEvent('R-HSA-5673001', 'ancestors')

# A list of participants for a given event
res = reactomeEvent('5205685', 'participants')

# A list of participating PhysicalEntities for a given event
res = reactomeEvent('R-HSA-5205685', 'participatingPhysicalEntities')

# A list of participating ReferenceEntities for a given event
res = reactomeEvent('5205685', 'participatingReferenceEntities')

VonWebEinstein/ReactomeAPI documentation built on May 9, 2019, 10:02 p.m.