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"addBiopaxInstance" ] }, { "page": "addBiopaxInstances", "title": "This function adds new instances to an existing biopax model.", "topics": [ "addBiopaxInstances" ] }, { "page": "addControl", "title": "This function adds a new control to the biopax model.", "topics": [ "addControl" ] }, { "page": "addhash", "title": "Adds a hash in front of a string", "topics": [ "addhash" ] }, { "page": "addns", "title": "Add a namespace tag to the supplied classname string", "topics": [ "addns" ] }, { "page": "addPathway", "title": "This function adds a new pathway to the biopax model.", "topics": [ "addPathway" ] }, { "page": "addPathwayComponents", "title": "This function adds pathway components to an existing pathway", "topics": [ "addPathwayComponents" ] }, { "page": "addPhysicalEntity", "title": "This function adds a new physical entity.", "topics": [ "addPhysicalEntity" ] }, { "page": "addPhysicalEntityParticipant", "title": "This function adds a new physical entity participant.", "topics": [ "addPhysicalEntityParticipant" ] }, { "page": "addPropertiesToBiopaxInstance", "title": "This function adds new properties to an existing biopax instance.", "topics": [ "addPropertiesToBiopaxInstance" ] }, { "page": "biopax", "title": "Biopax example data set", "topics": [ "biopax", "biopaxexample", "biopaxLevel3Example" ] }, { "page": "calcGraphOverlap", "title": "This function calculates the overlap of 2 graphs", "topics": [ "calcGraphOverlap" ] }, { "page": "checkValidity", "title": "This function checks the supplied biopax model for validity.", "topics": [ "checkValidity" ] }, { "page": "CLASS_INHERITANCE_BP2", "title": "CLASS_INHERITANCE_BP2", "topics": [ "CLASS_INHERITANCE_BP2" ] }, { "page": "CLASS_INHERITANCE_BP3", "title": "CLASS_INHERITANCE_BP3", "topics": [ "CLASS_INHERITANCE_BP3" ] }, { "page": "CLASS_PROPERTIES_BP2", "title": "CLASS_PROPERTIES_BP2", "topics": [ "CLASS_PROPERTIES_BP2" ] }, { "page": "CLASS_PROPERTIES_BP3", "title": "CLASS_PROPERTIES_BP3", "topics": [ "CLASS_PROPERTIES_BP3" ] }, { "page": "colorGraphNodes", "title": "This function colors the nodes of a graph.", "topics": [ "colorGraphNodes" ] }, { "page": "combineNodes", "title": "This function gracefully combines nodes of a regulatory graph.", "topics": [ "combineNodes" ] }, { "page": "createBiopax", "title": "This function creates a new Biopax model from scratch", "topics": [ "createBiopax" ] }, { "page": "DATABASE_BIOPAX", "title": "DATABASE_BIOPAX", "topics": [ "DATABASE_BIOPAX" ] }, { "page": "diffGraphs", "title": "This function returns the different nodes and edges between graph1 and graph2.", "topics": [ "diffGraphs" ] }, { "page": "downloadBiopaxData", "title": "This function downloads Biopax data from online databases", "topics": [ "downloadBiopaxData" ] }, { "page": "generateNewUniqueID", "title": "This function generates a new unique id for a biopax model", "topics": [ "generateNewUniqueID" ] }, { "page": "getClassProperties", "title": "This function returns the properties of the supplied biopax class.", "topics": [ "getClassProperties" ] }, { "page": "getInstanceClass", "title": "This function returns the class name of the instance.", "topics": [ "getInstanceClass" ] }, { "page": "getInstanceProperty", "title": "This function returns all properties of the specified type for an instance.", "topics": [ "getInstanceProperty" ] }, { "page": "getNeighborhood", "title": "This function returns the neighborhood of a physicalEntity", "topics": [ "getNeighborhood" ] }, { "page": "getParticipants", "title": "This function is used internally by pathway2Graph to obtain physical entities participating in an interaction.", "topics": [ "getParticipants" ] }, { "page": "getReferencedIDs", "title": "This function returns a vector of ids of all instances referenced by the specified instance.", "topics": [ "getReferencedIDs" ] }, { "page": "getReferencingIDs", "title": "This function returns a vector of ids of all instances that reference the supplied id.", "topics": [ "getReferencingIDs" ] }, { "page": "getSubClasses", "title": "This function returns the subclasses of the supplied biopax class.", "topics": [ "getSubClasses" ] }, { "page": "getSuperClasses", "title": "This function returns the superclasses of the supplied biopax class.", "topics": [ "getSuperClasses" ] }, { "page": "getXrefAnnotations", "title": "This function returns the annotations of the supplied instances.", "topics": [ "getXrefAnnotations" ] }, { "page": "hasProperty", "title": "Checks if instances in the biopax data.table have a given property", "topics": [ "hasProperty" ] }, { "page": "internal_checkArguments", "title": "This function checks the supplied arguments if they abid to the given restrictions", "topics": [ "internal_checkArguments" ] }, { "page": "internal_generateXMLfromBiopax", "title": "This function generates the xmlTree from the supplied biopax model.", "topics": [ "internal_generateXMLfromBiopax" ] }, { "page": "internal_getBiopaxModelAsDataFrame", "title": "This internal function parses the Biopax XML of the supplied biopax model and returns it in the data.frame format.", "topics": [ "internal_getBiopaxModelAsDataFrame" ] }, { "page": "internal_NrOfXMLNodes", "title": "This function is an internal function to count the Number of nodes and child nodes of an XMLNode.", "topics": [ "internal_NrOfXMLNodes" ] }, { "page": "internal_propertyListToDF", "title": "Internal function to build a data.frame from the list of properties for a new instance", "topics": [ "internal_propertyListToDF" ] }, { "page": "internal_resolvePhysicalEntityParticipant", "title": "This function resolves physicalEntityParticipantIDs to their corresponding physicalEntityIDs", "topics": [ "internal_resolvePhysicalEntityParticipant" ] }, { "page": "internal_XMLInstance2DF", "title": "This function is an internal function that parses a Biopax XMLNode.", "topics": [ "internal_XMLInstance2DF" ] }, { "page": "intersectGraphs", "title": "This function returns a graph computed by the insection of supplied graph1 and graph2.", "topics": [ "intersectGraphs" ] }, { "page": "isOfClass", "title": "Checks if instances in the biopax data.table are of the given class", "topics": [ "isOfClass" ] }, { "page": "isOfNamespace", "title": "Check if a classname is preceeded by a certain namespace tag like in \"namespace:classname\"", "topics": [ "isOfNamespace" ] }, { "page": "isURL", "title": "Check if a string is an URL, preceeded by \"http:\"", "topics": [ "isURL" ] }, { "page": "layoutRegulatoryGraph", "title": "This function generates a (more or less) beautiful layout for a regulatory graph.", "topics": [ "layoutRegulatoryGraph" ] }, { "page": "listComplexComponents", "title": "This function lists all components of a given complex.", "topics": [ "listComplexComponents" ] }, { "page": "listInstances", "title": "Lists all instances that conform to the selection criteria.", "topics": [ "listInstances" ] }, { "page": "listInteractionComponents", "title": "This function lists all components of a given interaction.", "topics": [ "listInteractionComponents" ] }, { "page": "listPathwayComponents", "title": "This function lists all pathway components of a given pathway.", "topics": [ "listPathwayComponents" ] }, { "page": "listPathways", "title": "This function returns a list of all pathway ids.", "topics": [ "listPathways" ] }, { "page": "mergePathways", "title": "This function merges two given pathways", "topics": [ "mergePathways" ] }, { "page": "pathway2AdjacancyMatrix", "title": "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.", "topics": [ "pathway2AdjacancyMatrix" ] }, { "page": "pathway2Geneset", "title": "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.", "topics": [ "pathway2Geneset" ] }, { "page": "pathway2Graph", "title": "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.", "topics": [ "pathway2Graph" ] }, { "page": "pathway2RegulatoryGraph", "title": "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.", "topics": [ "pathway2RegulatoryGraph" ] }, { "page": "plotRegulatoryGraph", "title": "This function layouts a regulatory graph and plots it using Rgraphviz.", "topics": [ "plotRegulatoryGraph" ] }, { "page": "print.biopax", "title": "Print a biopax object.", "topics": [ "print.biopax" ] }, { "page": "readBiopax", "title": "This function reads in a Biopax .owl file", "topics": [ "readBiopax" ] }, { "page": "removeDisconnectedParts", "title": "This function is used internally by pathway2Graph to remove the smaller disconnected parts of the pathway graph.", "topics": [ "removeDisconnectedParts" ] }, { "page": "removeInstance", "title": "This function removes an instance", "topics": [ "removeInstance" ] }, { "page": "removeNodes", "title": "This function gracefully removes nodes from a regulatory graph.", "topics": [ "removeNodes" ] }, { "page": "removeProperties", "title": "This function 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