mapId: Non-Reactome id mappings

In reactome/ReactomeContentService4R: Interface for the Reactome Content Service

Non-Reactome id mappings

Description

Mappings between non-Reactome identifiers and Reactome objects.

Usage

map2RefEntities(external.id)

map2Events(external.id, resource, species, mapTo = c("pathways", "reactions"))

event2Ids(event.id)

Arguments

external.id	an id from external dabatases, e.g. ChEBI, UniProt
resource	database name other than Reactome (e.g. UniProt, GeneCards)
species	name or taxon id or dbId or abbreviation of species
mapTo	retrieve Pathways or Reactions where an identifier can be mapped to
event.id	a stable or db id of an Event (Pathways and Reactions)

Details

Descriptions of functions:

• map2RefEntities maps a non-Reactome id to ReferenceEntities that store the given external id

• map2Events fetches Events related to a given non-Reactome id

• event2Ids gets all non-Reactome ids associated with a given Event

Value

a list of ReferenceEntity information

a dataframe of Events associated with the given id

non-Reactome ids associated with a given Event

Examples

## Not run: 
map2RefEntities("15377") #ChEBI id

## End(Not run)
map2Events("Q7Z569", resource="GeneCards", species="human", mapTo="reactions")
event2Ids("R-HSA-69541")

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