rBiopaxParser: Parses BioPax files and represents them in R
Version 2.16.0

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

AuthorFrank Kramer
Bioconductor views DataRepresentation
Date of publicationNone
MaintainerFrank Kramer <dev@frankkramer.de>
LicenseGPL (>= 2)
Version2.16.0
URL https://github.com/frankkramer-lab/rBiopaxParser
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("rBiopaxParser")

Getting started

Package overview
README.md

Popular man pages

addBiochemicalReaction: This function adds a new biochemical reaction to the biopax...
downloadBiopaxData: This function downloads Biopax data from online databases
getClassProperties: This function returns the properties of the supplied biopax...
getInstanceProperty: This function returns all properties of the specified type...
getParticipants: This function is used internally by pathway2Graph to obtain...
hasProperty: Checks if instances in the biopax data.table have a given...
pathway2RegulatoryGraph: This function generates the regulatory graph from the...
See all...

All man pages Function index File listing

Man pages

addBiochemicalReaction: This function adds a new biochemical reaction to the biopax...
addBiopaxInstance: This function adds a new instance to an existing biopax...
addBiopaxInstances: This function adds new instances to an existing biopax model.
addControl: This function adds a new control to the biopax model.
addhash: Adds a hash in front of a string
addns: Add a namespace tag to the supplied classname string
addPathway: This function adds a new pathway to the biopax model.
addPathwayComponents: This function adds pathway components to an existing pathway
addPhysicalEntity: This function adds a new physical entity.
addPhysicalEntityParticipant: This function adds a new physical entity participant.
addPropertiesToBiopaxInstance: This function adds new properties to an existing biopax...
biopax: Biopax example data set
calcGraphOverlap: This function calculates the overlap of 2 graphs
checkValidity: This function checks the supplied biopax model for validity.
CLASS_INHERITANCE_BP2: CLASS_INHERITANCE_BP2
CLASS_INHERITANCE_BP3: CLASS_INHERITANCE_BP3
CLASS_PROPERTIES_BP2: CLASS_PROPERTIES_BP2
CLASS_PROPERTIES_BP3: CLASS_PROPERTIES_BP3
colorGraphNodes: This function colors the nodes of a graph.
combineNodes: This function gracefully combines nodes of a regulatory...
createBiopax: This function creates a new Biopax model from scratch
DATABASE_BIOPAX: DATABASE_BIOPAX
diffGraphs: This function returns the different nodes and edges between...
downloadBiopaxData: This function downloads Biopax data from online databases
generateNewUniqueID: This function generates a new unique id for a biopax model
getClassProperties: This function returns the properties of the supplied biopax...
getInstanceClass: This function returns the class name of the instance.
getInstanceProperty: This function returns all properties of the specified type...
getNeighborhood: This function returns the neighborhood of a physicalEntity
getParticipants: This function is used internally by pathway2Graph to obtain...
getReferencedIDs: This function returns a vector of ids of all instances...
getReferencingIDs: This function returns a vector of ids of all instances that...
getSubClasses: This function returns the subclasses of the supplied biopax...
getSuperClasses: This function returns the superclasses of the supplied biopax...
getXrefAnnotations: This function returns the annotations of the supplied...
hasProperty: Checks if instances in the biopax data.table have a given...
internal_checkArguments: This function checks the supplied arguments if they abid to...
internal_generateXMLfromBiopax: This function generates the xmlTree from the supplied biopax...
internal_getBiopaxModelAsDataFrame: This internal function parses the Biopax XML of the supplied...
internal_NrOfXMLNodes: This function is an internal function to count the Number of...
internal_propertyListToDF: Internal function to build a data.frame from the list of...
internal_resolvePhysicalEntityParticipant: This function resolves physicalEntityParticipantIDs to their...
internal_XMLInstance2DF: This function is an internal function that parses a Biopax...
intersectGraphs: This function returns a graph computed by the insection of...
isOfClass: Checks if instances in the biopax data.table are of the given...
isOfNamespace: Check if a classname is preceeded by a certain namespace tag...
isURL: Check if a string is an URL, preceeded by "http:"
layoutRegulatoryGraph: This function generates a (more or less) beautiful layout for...
listComplexComponents: This function lists all components of a given complex.
listInstances: Lists all instances that conform to the selection criteria.
listInteractionComponents: This function lists all components of a given interaction.
listPathwayComponents: This function lists all pathway components of a given...
listPathways: This function returns a list of all pathway ids.
mergePathways: This function merges two given pathways
pathway2AdjacancyMatrix: This function generates an adjacency matrix from the...
pathway2Geneset: This function generates the gene set of a pathway. This...
pathway2Graph: This function generates a directed graph from all the...
pathway2RegulatoryGraph: This function generates the regulatory graph from the...
plotRegulatoryGraph: This function layouts a regulatory graph and plots it using...
print.biopax: Print a biopax object.
rBiopaxParser-package: Parses BioPax level files and represents them in R
readBiopax: This function reads in a Biopax .owl file
removeDisconnectedParts: This function is used internally by pathway2Graph to remove...
removeInstance: This function removes an instance
removeNodes: This function gracefully removes nodes from a regulatory...
removeProperties: This function removes a property
selectInstances: Returns all instances that conform to the selection criteria.
splitComplex: This functions splits up a complex into its components.
striphash: Strips a hash in front of a string
stripns: Strips a namespace tag off a supplied classname string
transitiveClosure: This function generates the transitive closure of the...
transitiveReduction: This function generates the transitive reduction of the...
unfactorize: Replace factors/levels in a data.frame and use plain strings...
uniteGraphs: This function unites two graphs.
writeBiopax: This function writes out a biopax model.

Functions

CLASS_INHERITANCE_BP2 Man page
CLASS_INHERITANCE_BP3 Man page
CLASS_PROPERTIES_BP2 Man page
CLASS_PROPERTIES_BP3 Man page
DATABASE_BIOPAX Man page
addBiochemicalReaction Man page Source code
addBiopaxInstance Man page Source code
addBiopaxInstances Man page Source code
addControl Man page Source code
addPathway Man page Source code
addPathwayComponents Man page Source code
addPhysicalEntity Man page Source code
addPhysicalEntityParticipant Man page Source code
addPropertiesToBiopaxInstance Man page Source code
addhash Man page Source code
addns Man page Source code
biopax Man page
biopaxLevel3Example Man page
biopaxexample Man page
calcGraphOverlap Man page Source code
checkValidity Man page Source code
colorGraphNodes Man page Source code
combineNodes Man page Source code
createBiopax Man page Source code
diffGraphs Man page Source code
downloadBiopaxData Man page Source code
generateNewUniqueID Man page Source code
getClassProperties Man page Source code
getInstanceClass Man page Source code
getInstanceProperty Man page Source code
getNeighborhood Man page Source code
getParticipants Man page Source code
getReferencedIDs Man page Source code
getReferencingIDs Man page Source code
getSubClasses Man page Source code
getSuperClasses Man page Source code
getXrefAnnotations Man page Source code
hasProperty Man page Source code
internal_NrOfXMLNodes Man page Source code
internal_XMLInstance2DF Man page Source code
internal_checkArguments Man page Source code
internal_generateXMLfromBiopax Man page Source code
internal_getBiopaxModelAsDataFrame Man page Source code
internal_propertyListToDF Man page Source code
internal_resolvePhysicalEntityParticipant Man page Source code
intersectGraphs Man page Source code
isOfClass Man page Source code
isOfNamespace Man page Source code
isURL Man page Source code
layoutRegulatoryGraph Man page Source code
listComplexComponents Man page Source code
listInstances Man page Source code
listInteractionComponents Man page Source code
listPathwayComponents Man page Source code
listPathways Man page Source code
mergePathways Man page Source code
pathway2AdjacancyMatrix Man page Source code
pathway2Geneset Man page Source code
pathway2Graph Man page Source code
pathway2RegulatoryGraph Man page Source code
plotRegulatoryGraph Man page Source code
print.biopax Man page Source code
rBiopaxParser Man page
rBiopaxParser-package Man page
readBiopax Man page Source code
removeDisconnectedParts Man page Source code
removeInstance Man page Source code
removeNodes Man page Source code
removeProperties Man page Source code
selectInstances Man page Source code
splitComplex Man page Source code
striphash Man page Source code
stripns Man page Source code
transitiveClosure Man page Source code
transitiveReduction Man page Source code
unfactorize Man page Source code
uniteGraphs Man page Source code
writeBiopax Man page Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/biopax2Classes.R
R/downloadBiopaxData.R
R/helperFunctions.R
R/modifyBiopax.R
R/parseBiopax.R
R/pathway2Graph.R
R/rBiopaxParser-package.R
R/selectBiopax.R
R/visualizeBiopax.R
R/writeBiopax.R
README.md
build
build/vignette.rds
data
data/biopaxLevel3Example.RData
data/biopaxexample.rda
inst
inst/CITATION
inst/doc
inst/doc/rBiopaxParserVignette.R
inst/doc/rBiopaxParserVignette.Rnw
inst/doc/rBiopaxParserVignette.pdf
inst/unitTests
inst/unitTests/test_biopax2Classes.R
inst/unitTests/test_downloadBiopaxData.R
inst/unitTests/test_helperFunctions.R
man
man/CLASS_INHERITANCE_BP2.Rd
man/CLASS_INHERITANCE_BP3.Rd
man/CLASS_PROPERTIES_BP2.Rd
man/CLASS_PROPERTIES_BP3.Rd
man/DATABASE_BIOPAX.Rd
man/addBiochemicalReaction.Rd
man/addBiopaxInstance.Rd
man/addBiopaxInstances.Rd
man/addControl.Rd
man/addPathway.Rd
man/addPathwayComponents.Rd
man/addPhysicalEntity.Rd
man/addPhysicalEntityParticipant.Rd
man/addPropertiesToBiopaxInstance.Rd
man/addhash.Rd
man/addns.Rd
man/biopax.Rd
man/calcGraphOverlap.Rd
man/checkValidity.Rd
man/colorGraphNodes.Rd
man/combineNodes.Rd
man/createBiopax.Rd
man/diffGraphs.Rd
man/downloadBiopaxData.Rd
man/generateNewUniqueID.Rd
man/getClassProperties.Rd
man/getInstanceClass.Rd
man/getInstanceProperty.Rd
man/getNeighborhood.Rd
man/getParticipants.Rd
man/getReferencedIDs.Rd
man/getReferencingIDs.Rd
man/getSubClasses.Rd
man/getSuperClasses.Rd
man/getXrefAnnotations.Rd
man/hasProperty.Rd
man/internal_NrOfXMLNodes.Rd
man/internal_XMLInstance2DF.Rd
man/internal_checkArguments.Rd
man/internal_generateXMLfromBiopax.Rd
man/internal_getBiopaxModelAsDataFrame.Rd
man/internal_propertyListToDF.Rd
man/internal_resolvePhysicalEntityParticipant.Rd
man/intersectGraphs.Rd
man/isOfClass.Rd
man/isOfNamespace.Rd
man/isURL.Rd
man/layoutRegulatoryGraph.Rd
man/listComplexComponents.Rd
man/listInstances.Rd
man/listInteractionComponents.Rd
man/listPathwayComponents.Rd
man/listPathways.Rd
man/mergePathways.Rd
man/pathway2AdjacancyMatrix.Rd
man/pathway2Geneset.Rd
man/pathway2Graph.Rd
man/pathway2RegulatoryGraph.Rd
man/plotRegulatoryGraph.Rd
man/print.biopax.Rd
man/rBiopaxParser-package.Rd
man/readBiopax.Rd
man/removeDisconnectedParts.Rd
man/removeInstance.Rd
man/removeNodes.Rd
man/removeProperties.Rd
man/selectInstances.Rd
man/splitComplex.Rd
man/striphash.Rd
man/stripns.Rd
man/transitiveClosure.Rd
man/transitiveReduction.Rd
man/unfactorize.Rd
man/uniteGraphs.Rd
man/writeBiopax.Rd
tests
tests/runTests.R
vignettes
vignettes/biopax2classgraph.pdf
vignettes/biopaxsimple.pdf
vignettes/mergedpw.pdf
vignettes/newpathways2.png
vignettes/rBiopaxParserVignette.Rnw
vignettes/segclock.pdf
vignettes/wntplot.pdf
rBiopaxParser documentation built on May 20, 2017, 10:14 p.m.

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