matchReferrals: MATCH biological referrals

In reactome/ReactomeGraph4R: Interface for the Reactome Graph Database

MATCH biological referrals

Description

This method retrieves Reactome objects that are connected with the given object in a reverse relationship. For example, to find Pathways containing the given Reaction.

Usage

matchReferrals(
  id = NULL,
  displayName = NULL,
  main = TRUE,
  depth = 1,
  all.depth = FALSE,
  species = NULL,
  type = c("row", "graph")
)

Arguments

id	stId or dbId of a Reactome object
displayName	displayName of a Reactome object
main	if set to TRUE, only first-class referrals returned
depth	number of depths
all.depth	if set to TRUE, connected objects in all depths returned
species	name or taxon id or dbId or abbreviation of a species
type	return results as a list of dataframes ('row'), or as a graph object ('graph')

Details

For now it just focuses on biological referrals in the following Classes: "Event", "PhysicalEntity", "Regulation", "CatalystActivity","ReferenceEntity" , "Interaction", "AbstractModifiedResidue".

Value

referrals of the given instance

See Also

Other match: matchDiseases(), matchHierarchy(), matchInteractors(), matchObject(), matchPEroles(), matchPaperObjects(), matchPrecedingAndFollowingEvents(), matchReactionsInPathway()

Examples

stId <- "R-HSA-112479"
# matchReferrals("R-HSA-112479", main=FALSE, all.depth=TRUE, type="row")

reactome/ReactomeGraph4R documentation built on May 15, 2023, 8:45 p.m.