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.

Author
Frank Kramer
Date of publication
None
Maintainer
Frank Kramer <dev@frankkramer.de>
License
GPL (>= 2)
Version
2.14.0
URLs

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