Package 'ReactomeGraph4R'

Title: Interface for the Reactome Graph Database
Description: Pathways, reactions, and biological entities in Reactome knowledge are systematically represented as an ordered network. Instances are represented as nodes and relationships between instances as edges; they are all stored in the Reactome Graph Database. This package serves as an interface to query the interconnected data from a local Neo4j database, with the aim of minimizing the usage of Neo4j Cypher queries.
Authors: Chi-Lam Poon [aut, cre] , Reactome [cph]
Maintainer: Chi-Lam Poon <[email protected]>
License: Apache License (>= 2)
Version: 1.15.0
Built: 2024-10-31 04:42:48 UTC
Source: https://github.com/bioc/ReactomeGraph4R

Help Index

Log in to the local neo4j server

Description

Before running login(), you have to successfully finish the Reactome Neo4j database setup and build a connection on your local machine (details see: https://github.com/reactome/ReactomeGraph4R). This command is to create a neo4r object that is used to communicate between R and Neo4j, also to do a sanity check for the connection.

Usage

login(con = NULL)

Arguments

con

an existed connexion object. It is not necessary to log in for the first time.

Value

connection to the local neo4j database

Examples

## Not run: 
# The first step to the graph database!
login()

## End(Not run)
# you can also check the neo4r connexion object by running:
getOption("con")

MATCH diseases of PhysicalEntity/Reaction/Pathway

Description

To find Diseases related to a PhysicalEntity or an Event, or get PhysicalEntities/Events associated with a Disease in reverse

Usage

matchDiseases(
  id = NULL,
  displayName = NULL,
  species = NULL,
  type = c("row", "graph")
)

Arguments

id

stId or dbId of a PhysicalEntity/Event/Disease
displayName

displayName of a PhysicalEntity/Event/Disease
species

name or taxon id or dbId or abbreviation of aspecies
type

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

Value

Disease(s) related to the given PhysicalEntity/Reaction/Pathway; or instances related to the given Disease

See Also

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

Examples

disease <- "neuropathy"
# matchDiseases(displayName=disease, species="M. musculus", type="row")
# matchDiseases(id="R-HSA-162588", type="graph")

MATCH hierarchy

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

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

## 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")

MATCH interactors

Description

To retrieve interactions of a given PhysicalEntity (PE), it first finds the ReferenceEntity matched with the PE, then get the Interactions having "interactor" relationship with the ReferenceEntity.

Usage

matchInteractors(
  pe.id = NULL,
  pe.displayName = NULL,
  species = NULL,
  type = c("row", "graph")
)

Arguments

pe.id

stId or dbId of a PhysicalEntity
pe.displayName

displayName of a PhysicalEntity
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

interactions of a given PhysicalEntity

See Also

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

Examples

pe.id <- 996766
# matchInteractors(pe.id)

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)

MATCH objects related to a paper

Description

Fetch Reactome instances related to a paper by its PubMed id or title

Usage

matchPaperObjects(
  pubmed.id = NULL,
  displayName = NULL,
  type = c("row", "graph")
)

Arguments

pubmed.id

PubMed identifier of a paper
displayName

paper title
type

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

Value

Reactome instances associated with a paper

See Also

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

Examples

## fetch Reactome instances by paper title
paper <- "Chaperone-mediated autophagy at a glance"
# matchPaperObjects(displayName=paper)

## fetch Reactome instances by pubmed id
# matchPaperObjects(pubmed.id="20797626", type="graph")
# matchPaperObjects(pubmed.id="23515720", type="row")

MATCH roles of PhysicalEntity

Description

This function retrieves the role(s) of a given PhysicalEntity including:

  • Input

  • Output

  • Regulator

  • Catalyst

Usage

matchPEroles(
  pe.id = NULL,
  pe.displayName = NULL,
  species = NULL,
  type = c("row", "graph")
)

Arguments

pe.id

stId or dbId of a PhysicalEntity
pe.displayName

displayName of a PhysicalEntity
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')

Value

information of the given PhysicalEntity and its role(s)

See Also

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

Examples

stId <- "R-HSA-8944354"
# matchPEroles(pe.id = stId, type = "graph")

# matchPEroles(pe.displayName = "2SUMO1:MITF [nucleoplasm]", 
#              species = "pig", type = "row")

MATCH the preceding/following Events

Description

This method can find preceding and following ReactionLikeEvents (RLEs) of a specific Event with the relationship 'precedingEvent'. The argument "depth" is used to describe the "variable length relationships" in Neo4j, default is 1 (i.e. immediately connected); or you can set all.depth = TRUE to retrieve the whole context.

Usage

matchPrecedingAndFollowingEvents(
  event.id = NULL,
  event.displayName = NULL,
  species = NULL,
  depth = 1,
  all.depth = FALSE,
  type = c("row", "graph")
)

Arguments

event.id

stId/dbId of an Event
event.displayName

displayName of an Event
species

name or taxon id or dbId or abbreviation of specified species
depth

number of depths
all.depth

if set to TRUE, all RLE(s) connected to the given Event in all depths returned
type

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

Value

preceding/following Events connected to the given Event in specified depth(s), default depth = 1

See Also

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

Examples

stId <- "R-HSA-983150"
# matchPrecedingAndFollowingEvents(event.id=stId, depth=2, type="row")

MATCH Reactions in associated Pathway

Description

This method could find all Reactions connected with a given Pathway by the relationship 'hasEvent'. Also, the input can be a Reaction, the result would then be Pathway(s) linked via 'hasEvent' together with other Reactions linked with the Pathways(s).

Usage

matchReactionsInPathway(
  event.id = NULL,
  event.displayName = NULL,
  species = NULL,
  type = c("row", "graph")
)

Arguments

event.id

stId or dbId of an Event
event.displayName

displayName of an Event
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')

Value

Reactions connected to the given Pathway/Reaction via 'hasEvent' relationships

See Also

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

Examples

reaction <- "R-HSA-1369062"
# matchReactionsInPathway(event.id=reaction, type="graph")
# matchReactionsInPathway("R-HSA-5682285", type="row")

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")

Retrieve multiple Reactome objects

Description

The matchObject function takes only one id/name at a time, this method allows you to input many ids and get an aggregated table for their detailed information. It can only accept ids for now.

Usage

multiObjects(ids, databaseName = "Reactome", speedUp = FALSE, cluster = 2)

Arguments

ids

Reactome stIds/dbIds, or non-Reactome ids
databaseName

database name
speedUp

set TRUE to use doParallel method
cluster

the number of cluster in makeCluster

Value

Reactome database objects for the given ids

See Also

matchObject for details

Examples

## "ids" can be Reactome or non-Reactome ids
ids <- c("P02741", "P08887", "P08505", "Q9GZQ8")
#res <- multiObjects(ids, databaseName="UniProt", speedUp=TRUE)

Unnest a column of lists in a dataframe

Description

Unnest a column of lists in a dataframe

Usage

unnestListCol(df, column = "properties")

Arguments

df

dataframe where a column to be unnested
column

specific column to be unnested

Value

an unnested dataframe for network visualization

Examples

# nodes <- unnestListCol(graph$nodes, "properties")