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.

AuthorFrank Kramer
Date of publicationNone
MaintainerFrank Kramer <dev@frankkramer.de>
LicenseGPL (>= 2)
Version2.14.0
https://github.com/frankkramer-lab/rBiopaxParser

View on Bioconductor

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.

Files in this package

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

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