CLASS_INHERITANCE_BP2   CLASS_INHERITANCE_BP2
CLASS_INHERITANCE_BP3   CLASS_INHERITANCE_BP3
CLASS_PROPERTIES_BP2    CLASS_PROPERTIES_BP2
CLASS_PROPERTIES_BP3    CLASS_PROPERTIES_BP3
DATABASE_BIOPAX         DATABASE_BIOPAX
addBiochemicalReaction
                        This function adds a new biochemical reaction
                        to the biopax model.
addBiopaxInstance       This function adds a new instance to an
                        existing biopax model.
addBiopaxInstances      This function adds new instances to an existing
                        biopax model.
addControl              This function adds a new control to the biopax
                        model.
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 instance.
addhash                 Adds a hash in front of a string
addns                   Add a namespace tag to the supplied classname
                        string
biopax                  Biopax example data set
calcGraphOverlap        This function calculates the overlap of 2
                        graphs
checkValidity           This function checks the supplied biopax model
                        for validity.
colorGraphNodes         This function colors the nodes of a graph.
combineNodes            This function gracefully combines nodes of a
                        regulatory graph.
createBiopax            This function creates a new Biopax model from
                        scratch
diffGraphs              This function returns the different nodes and
                        edges between graph1 and graph2.
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 class.
getInstanceClass        This function returns the class name of the
                        instance.
getInstanceProperty     This function returns all properties of the
                        specified type for an instance.
getNeighborhood         This function returns the neighborhood of a
                        physicalEntity
getReferencedIDs        This function returns a vector of ids of all
                        instances referenced by the specified instance.
getReferencingIDs       This function returns a vector of ids of all
                        instances that reference the supplied id.
getSubClasses           This function returns the subclasses of the
                        supplied biopax class.
getSuperClasses         This function returns the superclasses of the
                        supplied biopax class.
getXrefAnnotations      This function returns the annotations of the
                        supplied instances.
hasProperty             Checks if instances in the biopax data.frame
                        have a given property
internal_NrOfXMLNodes   This function in an internal function to count
                        the Number of nodes and child nodes of an
                        XMLNode.
internal_XMLInstance2DF
                        This function in an internal function that
                        parses a Biopax Level 2 XMLNode.
internal_checkArguments
                        This function checks the supplied arguments if
                        they abid to the given restrictions
internal_generateXMLfromBiopax
                        This function generates the xmlTree from the
                        supplied biopax model.
internal_getBiopaxModelAsDataFrame
                        This internal function parses the Biopax XML of
                        the supplied biopax model and returns it in the
                        data.frame format.
internal_getInstanceProperty_df
                        This function returns all properties of the
                        specified type for an instance.
internal_propertyListToDF
                        Internal function to build a data.frame from
                        the list of properties for a new instance
internal_resolvePhysicalEntityParticipant
                        This function resolves
                        physicalEntityParticipantIDs to their
                        corresponding physicalEntityIDs
intersectGraphs         This function returns a graph computed by the
                        insection of supplied graph1 and graph2.
isOfClass               Checks if instances in the biopax data.frame
                        are of the given class
isOfNamespace           Check if a classname is preceeded by a certain
                        namespace tag like in "namespace:classname"
layoutRegulatoryGraph   This function generates a (more or less)
                        beautiful layout for a regulatory graph.
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 pathway.
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 activations/inhibitions of a pathway
                        in a biopax model.
pathway2Geneset         This function generates the gene set of a
                        pathway.
pathway2RegulatoryGraph
                        This function generates the regulatory graph
                        from the activations/inhibitions of a pathway
                        in a biopax model.
plotRegulatoryGraph     This function layouts a regulatory graph and
                        plots it using Rgraphviz.
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
removeInstance          This function removes an instance
removeNodes             This function gracefully removes nodes from a
                        regulatory graph.
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 supplied graph.
transitiveReduction     This function generates the transitive
                        reduction of the supplied graph.
unfactorize             Replace factors/levels in a data.frame and use
                        plain strings instead
uniteGraphs             This function unites two graphs.
writeBiopax             This function writes out a biopax model.
