matchObject: Basic query for database objects

In reactome/ReactomeGraph4R: Interface for the Reactome Graph Database

Basic query for database objects

Description

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

Usage

matchObject(
  id = NULL,
  displayName = NULL,
  schemaClass = NULL,
  species = NULL,
  returnedAttributes = NULL,
  property = NULL,
  relationship = NULL,
  limit = NULL,
  databaseName = "Reactome"
)

Arguments

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 NULL, all attributes returned
property	a list of property keys and values, e.g. list(isChimeric = TRUE, isInDisease = TRUE)
relationship	relationship type(s)
limit	the number of returned objects
databaseName	database name. All databases see here

Value

Reactome database object(s) that meets all specified conditions

See Also

multiObjects for multiple ids

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

Examples

## 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)
    

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