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| rBiopaxParser-package | Parses BioPax level files and represents them in R |
| 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. |
| 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 instance. |
| biopax | Biopax example data set |
| biopaxexample | Biopax example data set |
| biopaxLevel3Example | 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 graph. |
| createBiopax | This function creates a new Biopax model from scratch |
| DATABASE_BIOPAX | DATABASE_BIOPAX |
| 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 |
| getParticipants | This function is used internally by pathway2Graph to obtain physical entities participating in an interaction. |
| 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.table have a given property |
| 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_NrOfXMLNodes | This function is an internal function to count the Number of nodes and child nodes of an XMLNode. |
| 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 |
| internal_XMLInstance2DF | This function is an internal function that parses a Biopax XMLNode. |
| intersectGraphs | This function returns a graph computed by the insection of supplied graph1 and graph2. |
| isOfClass | Checks if instances in the biopax data.table are of the given class |
| isOfNamespace | Check if a classname is preceeded by a certain namespace tag like in "namespace:classname" |
| isURL | Check if a string is an URL, preceeded by "http:" |
| 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. This function internally first calls pathway2RegulatoryGraph, then converts the regulatory graph to an adjacency matrix. See pathway2RegulatoryGraph for more details. |
| pathway2Geneset | This function generates the gene set of a pathway. This function generates a gene set of all physicalEntity's of a pathway. First all interactions of the pathway are retrieved and all components of these interactions are then listed. |
| pathway2Graph | This function generates a directed graph from all the interactions of a specified pathway in a biopax model. Edges with no direction are indicated by a 0 weight. |
| pathway2RegulatoryGraph | This function generates the regulatory graph from the activations/inhibitions of a pathway in a biopax model. This functions builds a graph from the pathway components of the supplied pathway. Only instances of class 'control' are considered, this leads a functinal graph with all edges either representing activations or inhibitions. No transports, no translocation, etc. If desired complexes can be split up into several nodes, this can sometimes lead to a more complex and cluttered graph. There can not be multiple edges between 2 nodes. Whenever duplicated edges are generated (especially by splitting up complexes) a warning is thrown. |
| plotRegulatoryGraph | This function layouts a regulatory graph and plots it using Rgraphviz. |
| print.biopax | Print a biopax object. |
| rBiopaxParser | 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 the smaller disconnected parts of the pathway graph. |
| 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. |