matchObject {ReactomeGraph4R} | R Documentation |
This function can fetch instance by setting the following arguments:
id: a Reactome dbId/stId, or non-Reactome id (e.g. UniProt)
displayName: a display name of a Reactome object
schemaClass: a specific schema class, see Data Schema
property: a property of a node or relationship, access the full
list of properties: con <- getOption("con"); con$get_property_keys()
relationship: a relationship between nodes, access the full
list of relationships: con <- getOption("con"); con$get_relationships()
Species information can see
here, or run
View(matchObject(schemaClass = "Species")[['databaseObject']])
to view a
full table
matchObject( id = NULL, displayName = NULL, schemaClass = NULL, species = NULL, returnedAttributes = NULL, property = NULL, relationship = NULL, limit = NULL, databaseName = "Reactome" )
id |
Reactome stId or dbId, or non-Reactome identifier |
displayName |
displayName of a database object |
schemaClass |
schema class of a database object |
species |
name or taxon id or dbId or abbreviation of specified species |
returnedAttributes |
specific attribute(s) to be returned.
If set to |
property |
a list of property keys and values,
e.g. |
relationship |
relationship type(s) |
limit |
the number of returned objects |
databaseName |
database name. All databases see here |
Reactome database object(s) that meets all specified conditions
multiObjects for multiple ids
Other match:
matchDiseases()
,
matchHierarchy()
,
matchInteractors()
,
matchPEroles()
,
matchPaperObjects()
,
matchPrecedingAndFollowingEvents()
,
matchReactionsInPathway()
,
matchReferrals()
## fetch instance by class # all.species <- matchObject(schemaClass = "Species") ## fetch instance by name # matchObject(displayName = "RCOR1 [nucleoplasm]", # returnedAttributes=c("stId", "speciesName")) ## fetch instance by id ## Reactome id # matchObject(id = "R-HSA-9626034") ## non-Reactome id # matchObject(id = "P60484", databaseName = "UniProt") ## fecth instances by relationship # matchObject(relationship="inferredTo", limit=10) ## fetch instances by property property.list <- list(hasEHLD = TRUE, isInDisease = TRUE) # matchObject(property = property.list, # returnedAttributes = c("displayName", "stId", "isInDisease", "hasEHLD"), # limit=20)