Package: rBiopaxParser 2.51.0

Frank Kramer

rBiopaxParser: Parses BioPax files and represents them in R

Parses BioPAX files and represents them in R, at the moment BioPAX level 2 and level 3 are supported.

Authors:Frank Kramer

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NEWS

# Install 'rBiopaxParser' in R:

install.packages('rBiopaxParser', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/frankkramer-lab/rbiopaxparser/issues

Datasets:

biopax - Biopax example data set
biopaxLevel3Example - Biopax example data set

On BioConductor:rBiopaxParser-2.51.0(bioc 3.23)rBiopaxParser-2.50.0(bioc 3.22)

datarepresentation

5.85 score 10 stars 8 scripts 502 downloads 7 mentions 55 exports 2 dependencies

Last updated from:aed165a3b9. Checks:1 ERROR, 6 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	142
linux-devel-x86_64	NOTE	188
source / vignettes	OK	200
linux-release-x86_64	NOTE	166
macos-devel-arm64	NOTE	103
macos-release-arm64	NOTE	118
windows-devel	NOTE	147
windows-release	NOTE	112
wasm-release	OK	120

Exports:addBiochemicalReaction addBiopaxInstance addBiopaxInstances addControl addPathway addPathwayComponents addPhysicalEntity addPhysicalEntityParticipant addPropertiesToBiopaxInstance calcGraphOverlap CLASS_INHERITANCE_BP2 CLASS_INHERITANCE_BP3 CLASS_PROPERTIES_BP2 CLASS_PROPERTIES_BP3 colorGraphNodes combineNodes createBiopax DATABASE_BIOPAX diffGraphs downloadBiopaxData generateNewUniqueID getClassProperties getInstanceClass getInstanceProperty getNeighborhood getReferencedIDs getReferencingIDs getSubClasses getSuperClasses getXrefAnnotations hasProperty intersectGraphs isOfClass layoutRegulatoryGraph listComplexComponents listInstances listInteractionComponents listPathwayComponents listPathways mergePathways pathway2AdjacancyMatrix pathway2Geneset pathway2Graph pathway2RegulatoryGraph plotRegulatoryGraph readBiopax removeInstance removeNodes removeProperties selectInstances splitComplex transitiveClosure transitiveReduction uniteGraphs writeBiopax

Dependencies:data.table XML

rBiopaxParser Vignette

Rendered fromrBiopaxParserVignette.Rnwusingutils::Sweaveon Mar 26 2026.

Last update: 2020-07-15
Started: 2013-11-01

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Parses BioPax level files and represents them in R	rBiopaxParser-package rBiopaxParser
This function adds a new biochemical reaction to the biopax model.	addBiochemicalReaction
This function adds a new instance to an existing biopax model.	addBiopaxInstance
This function adds new instances to an existing biopax model.	addBiopaxInstances
This function adds a new control to the biopax model.	addControl
Adds a hash in front of a string	addhash
Add a namespace tag to the supplied classname string	addns
This function adds a new pathway to the biopax model.	addPathway
This function adds pathway components to an existing pathway	addPathwayComponents
This function adds a new physical entity.	addPhysicalEntity
This function adds a new physical entity participant.	addPhysicalEntityParticipant
This function adds new properties to an existing biopax instance.	addPropertiesToBiopaxInstance
Biopax example data set	biopax biopaxexample biopaxLevel3Example
This function calculates the overlap of 2 graphs	calcGraphOverlap
This function checks the supplied biopax model for validity.	checkValidity
CLASS_INHERITANCE_BP2	CLASS_INHERITANCE_BP2
CLASS_INHERITANCE_BP3	CLASS_INHERITANCE_BP3
CLASS_PROPERTIES_BP2	CLASS_PROPERTIES_BP2
CLASS_PROPERTIES_BP3	CLASS_PROPERTIES_BP3
This function colors the nodes of a graph.	colorGraphNodes
This function gracefully combines nodes of a regulatory graph.	combineNodes
This function creates a new Biopax model from scratch	createBiopax
DATABASE_BIOPAX	DATABASE_BIOPAX
This function returns the different nodes and edges between graph1 and graph2.	diffGraphs
This function downloads Biopax data from online databases	downloadBiopaxData
This function generates a new unique id for a biopax model	generateNewUniqueID
This function returns the properties of the supplied biopax class.	getClassProperties
This function returns the class name of the instance.	getInstanceClass
This function returns all properties of the specified type for an instance.	getInstanceProperty
This function returns the neighborhood of a physicalEntity	getNeighborhood
This function is used internally by pathway2Graph to obtain physical entities participating in an interaction.	getParticipants
This function returns a vector of ids of all instances referenced by the specified instance.	getReferencedIDs
This function returns a vector of ids of all instances that reference the supplied id.	getReferencingIDs
This function returns the subclasses of the supplied biopax class.	getSubClasses
This function returns the superclasses of the supplied biopax class.	getSuperClasses
This function returns the annotations of the supplied instances.	getXrefAnnotations
Checks if instances in the biopax data.table have a given property	hasProperty
This function checks the supplied arguments if they abid to the given restrictions	internal_checkArguments
This function generates the xmlTree from the supplied biopax model.	internal_generateXMLfromBiopax
This internal function parses the Biopax XML of the supplied biopax model and returns it in the data.frame format.	internal_getBiopaxModelAsDataFrame
This function is an internal function to count the Number of nodes and child nodes of an XMLNode.	internal_NrOfXMLNodes
Internal function to build a data.frame from the list of properties for a new instance	internal_propertyListToDF
This function resolves physicalEntityParticipantIDs to their corresponding physicalEntityIDs	internal_resolvePhysicalEntityParticipant
This function is an internal function that parses a Biopax XMLNode.	internal_XMLInstance2DF
This function returns a graph computed by the insection of supplied graph1 and graph2.	intersectGraphs
Checks if instances in the biopax data.table are of the given class	isOfClass
Check if a classname is preceeded by a certain namespace tag like in "namespace:classname"	isOfNamespace
Check if a string is an URL, preceeded by "http:"	isURL
This function generates a (more or less) beautiful layout for a regulatory graph.	layoutRegulatoryGraph
This function lists all components of a given complex.	listComplexComponents
Lists all instances that conform to the selection criteria.	listInstances
This function lists all components of a given interaction.	listInteractionComponents
This function lists all pathway components of a given pathway.	listPathwayComponents
This function returns a list of all pathway ids.	listPathways
This function merges two given pathways	mergePathways
This function generates an adjacency matrix from the activations/inhibitions of a pathway in a biopax model. This function internally first calls pathway2RegulatoryGraph, then converts the regulatory graph to an adjacency matrix. See pathway2RegulatoryGraph for more details.	pathway2AdjacancyMatrix
This function generates the gene set of a pathway. This function generates a gene set of all physicalEntity's of a pathway. First all interactions of the pathway are retrieved and all components of these interactions are then listed.	pathway2Geneset
This function generates a directed graph from all the interactions of a specified pathway in a biopax model. Edges with no direction are indicated by a 0 weight.	pathway2Graph
This function generates the regulatory graph from the activations/inhibitions of a pathway in a biopax model. This functions builds a graph from the pathway components of the supplied pathway. Only instances of class 'control' are considered, this leads a functinal graph with all edges either representing activations or inhibitions. No transports, no translocation, etc. If desired complexes can be split up into several nodes, this can sometimes lead to a more complex and cluttered graph. There can not be multiple edges between 2 nodes. Whenever duplicated edges are generated (especially by splitting up complexes) a warning is thrown.	pathway2RegulatoryGraph
This function layouts a regulatory graph and plots it using Rgraphviz.	plotRegulatoryGraph
Print a biopax object.	print.biopax
This function reads in a Biopax .owl file	readBiopax
This function is used internally by pathway2Graph to remove the smaller disconnected parts of the pathway graph.	removeDisconnectedParts
This function removes an instance	removeInstance
This function gracefully removes nodes from a regulatory graph.	removeNodes
This function removes a property	removeProperties
Returns all instances that conform to the selection criteria.	selectInstances
This functions splits up a complex into its components.	splitComplex
Strips a hash in front of a string	striphash
Strips a namespace tag off a supplied classname string	stripns
This function generates the transitive closure of the supplied graph.	transitiveClosure
This function generates the transitive reduction of the supplied graph.	transitiveReduction
Replace factors/levels in a data.frame and use plain strings instead	unfactorize
This function unites two graphs.	uniteGraphs
This function writes out a biopax model.	writeBiopax