Man pages for rBiopaxParser
Parses BioPax files and represents them in R

addBiochemicalReactionThis function adds a new biochemical reaction to the biopax...
addBiopaxInstanceThis function adds a new instance to an existing biopax...
addBiopaxInstancesThis function adds new instances to an existing biopax model.
addControlThis function adds a new control to the biopax model.
addhashAdds a hash in front of a string
addnsAdd a namespace tag to the supplied classname string
addPathwayThis function adds a new pathway to the biopax model.
addPathwayComponentsThis function adds pathway components to an existing pathway
addPhysicalEntityThis function adds a new physical entity.
addPhysicalEntityParticipantThis function adds a new physical entity participant.
addPropertiesToBiopaxInstanceThis function adds new properties to an existing biopax...
biopaxBiopax example data set
calcGraphOverlapThis function calculates the overlap of 2 graphs
checkValidityThis function checks the supplied biopax model for validity.
CLASS_INHERITANCE_BP2CLASS_INHERITANCE_BP2
CLASS_INHERITANCE_BP3CLASS_INHERITANCE_BP3
CLASS_PROPERTIES_BP2CLASS_PROPERTIES_BP2
CLASS_PROPERTIES_BP3CLASS_PROPERTIES_BP3
colorGraphNodesThis function colors the nodes of a graph.
combineNodesThis function gracefully combines nodes of a regulatory...
createBiopaxThis function creates a new Biopax model from scratch
DATABASE_BIOPAXDATABASE_BIOPAX
diffGraphsThis function returns the different nodes and edges between...
downloadBiopaxDataThis function downloads Biopax data from online databases
generateNewUniqueIDThis function generates a new unique id for a biopax model
getClassPropertiesThis function returns the properties of the supplied biopax...
getInstanceClassThis function returns the class name of the instance.
getInstancePropertyThis function returns all properties of the specified type...
getNeighborhoodThis function returns the neighborhood of a physicalEntity
getParticipantsThis function is used internally by pathway2Graph to obtain...
getReferencedIDsThis function returns a vector of ids of all instances...
getReferencingIDsThis function returns a vector of ids of all instances that...
getSubClassesThis function returns the subclasses of the supplied biopax...
getSuperClassesThis function returns the superclasses of the supplied biopax...
getXrefAnnotationsThis function returns the annotations of the supplied...
hasPropertyChecks if instances in the biopax data.table have a given...
internal_checkArgumentsThis function checks the supplied arguments if they abid to...
internal_generateXMLfromBiopaxThis function generates the xmlTree from the supplied biopax...
internal_getBiopaxModelAsDataFrameThis internal function parses the Biopax XML of the supplied...
internal_NrOfXMLNodesThis function is an internal function to count the Number of...
internal_propertyListToDFInternal function to build a data.frame from the list of...
internal_resolvePhysicalEntityParticipantThis function resolves physicalEntityParticipantIDs to their...
internal_XMLInstance2DFThis function is an internal function that parses a Biopax...
intersectGraphsThis function returns a graph computed by the insection of...
isOfClassChecks if instances in the biopax data.table are of the given...
isOfNamespaceCheck if a classname is preceeded by a certain namespace tag...
isURLCheck if a string is an URL, preceeded by "http:"
layoutRegulatoryGraphThis function generates a (more or less) beautiful layout for...
listComplexComponentsThis function lists all components of a given complex.
listInstancesLists all instances that conform to the selection criteria.
listInteractionComponentsThis function lists all components of a given interaction.
listPathwayComponentsThis function lists all pathway components of a given...
listPathwaysThis function returns a list of all pathway ids.
mergePathwaysThis function merges two given pathways
pathway2AdjacancyMatrixThis function generates an adjacency matrix from the...
pathway2GenesetThis function generates the gene set of a pathway. This...
pathway2GraphThis function generates a directed graph from all the...
pathway2RegulatoryGraphThis function generates the regulatory graph from the...
plotRegulatoryGraphThis function layouts a regulatory graph and plots it using...
print.biopaxPrint a biopax object.
rBiopaxParser-packageParses BioPax level files and represents them in R
readBiopaxThis function reads in a Biopax .owl file
removeDisconnectedPartsThis function is used internally by pathway2Graph to remove...
removeInstanceThis function removes an instance
removeNodesThis function gracefully removes nodes from a regulatory...
removePropertiesThis function removes a property
selectInstancesReturns all instances that conform to the selection criteria.
splitComplexThis functions splits up a complex into its components.
striphashStrips a hash in front of a string
stripnsStrips a namespace tag off a supplied classname string
transitiveClosureThis function generates the transitive closure of the...
transitiveReductionThis function generates the transitive reduction of the...
unfactorizeReplace factors/levels in a data.frame and use plain strings...
uniteGraphsThis function unites two graphs.
writeBiopaxThis function writes out a biopax model.
rBiopaxParser documentation built on Nov. 17, 2017, 1:41 p.m.