matchHierarchy: MATCH hierarchy

Description Usage Arguments Value See Also Examples

View source: R/queries.R

Description

Reactome data are organized in a hierarchical way: Pathway-Reaction-Entity. This function retrieves the hierarchical data of a given Event (Pathway or Reaction) or Entity (PhysicalEntity or ReferenceEntity).

Usage

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matchHierarchy(
  id = NULL,
  displayName = NULL,
  databaseName = "Reactome",
  species = NULL,
  type = c("row", "graph")
)

Arguments

id

stId or dbId of an Event/Entity; or an external id

displayName

displayName of Event/PhysicalEntity/ReferenceEntity

databaseName

database name

species

name or taxon id or dbId or abbreviation of specified species

type

return results as a list of dataframes ('row'), or as a graph object ('graph')

Value

hierarchical instances of the given id and databaseName

See Also

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

Examples

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## use the Reactome displayName of a UniProt object
uniprot.name <- "UniProt:P04637 TP53"
# matchHierarchy(displayName=uniprot.name, 
#                databaseName="UniProt", type="row")
# matchHierarchy(id="R-HSA-1369062", type="graph")

reactome/ReactomeGraph4R documentation built on May 29, 2021, 7:42 a.m.