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"Coercions between matrix and graph representations", "topics": [ "aM2bpG", "coerce,graphNEL,matrix-method", "coerce,matrix,graphNEL-method", "ftM2adjM", "ftM2graphNEL" ] }, { "page": "combineNodes", "title": "combineNodes", "topics": [ "combineNodes", "combineNodes,character,graphNEL,character-method" ] }, { "page": "DFS", "title": "Depth First Search", "topics": [ "DFS", "DFS,graph,character-method" ] }, { "page": "distGraph-class", "title": "Class \"distGraph\"", "topics": [ "adj,distGraph,ANY-method", "Dist", "Dist,distGraph-method", "distGraph-class", "edgeL,distGraph-method", "edges,distGraph-method", "edgeWeights,distGraph,ANY-method", "edgeWeights,distGraph-method", "initialize,distGraph-method", "nodes,distGraph-method", "numNodes,distGraph-method", "show,distGraph-method", "threshold", "threshold,distGraph-method", "[.dist" ] }, { "page": "duplicatedEdges", "title": "duplicatedEdges", "topics": [ "duplicatedEdges" ] }, { "page": "edgeData-methods", "title": "Get and set attributes for the edges of a graph object", "topics": [ "edgeData", "edgeData-methods", "edgeData<-", "edgeData<--methods" ] }, { "page": "edgeDataDefaults-methods", "title": "Get and set default attributes for the edges of a graph", "topics": [ "edgeDataDefaults", "edgeDataDefaults-methods", "edgeDataDefaults<-", "edgeDataDefaults<--methods" ] }, { "page": "edgeMatrix", "title": "Compute an Edge Matrix or weight vector for a Graph", "topics": [ "edgeMatrix", "edgeMatrix,clusterGraph-method", "edgeMatrix,distGraph-method", "edgeMatrix,graphAM-method", "edgeMatrix,graphBAM-method", "edgeMatrix,graphNEL-method", "eWV", "pathWeights" ] }, { "page": "edgeSets", "title": "MultiGraph edgeSet data", "topics": [ "esetsFemale", "esetsMale" ] }, { "page": "edgeWeights", "title": "Retrieve the edge weights of a graph", "topics": [ "edgeWeights" ] }, { "page": "fromGXL-methods", "title": "Methods for GXL manipulations in package graph", "topics": [ "dumpGXL", "dumpGXL,connection-method", "dumpGXL-methods", "fromGXL", "fromGXL,connection-method", "fromGXL-methods", "GXL", "gxlTreeNEL", "NELhandler", "toGXL", "toGXL-methods", "validateGXL", "validateGXL,connection-method" ] }, { "page": "graph-class", "title": "Class \"graph\"", "topics": [ "complement", "complement,graph-method", "connComp", "connComp,graph-method", "degree", "degree,graph-method", "degree,MultiGraph-method", "dfs,graph-method", "edgeData,graph,character,character,character-method", "edgeData,graph,character,character,missing-method", "edgeData,graph,character,missing,character-method", "edgeData,graph,missing,character,character-method", "edgeData,graph,missing,missing,character-method", "edgeData,graph,missing,missing,missing-method", "edgeData<-,graph,character,character,character,ANY-method", "edgeData<-,graph,character,character,character-method", "edgeData<-,graph,character,missing,character,ANY-method", "edgeData<-,graph,character,missing,character-method", "edgeData<-,graph,missing,character,character,ANY-method", "edgeData<-,graph,missing,character,character-method", "edgeDataDefaults,graph,character-method", "edgeDataDefaults,graph,missing-method", "edgeDataDefaults<-,graph,character,ANY-method", "edgeDataDefaults<-,graph,character-method", "edgeDataDefaults<-,graph,missing,list-method", "edgeL,graph-method", "edgemode", "edgemode,graph-method", "edgemode<-", "edgemode<-,graph,character-method", "edgeNames", "edgeNames,graph-method", "edgeWeights,graph,character-method", "edgeWeights,graph,missing-method", "edgeWeights,graph,numeric-method", "graph-class", "graphBase-class", "intersection", "intersection,graph,graph-method", "intersection2", "intersection2,graph,graph-method", "isAdjacent,graph,character,character-method", "isConnected", "isConnected,graph-method", "isDirected,graph-method", "join", "join,graph,graph-method", "nodeData,graph,character,character-method", "nodeData,graph,character,missing-method", "nodeData,graph,missing,character-method", "nodeData,graph,missing,missing-method", "nodeData<-,graph,character,character-method", "nodeData<-,graph,missing,character-method", "nodeDataDefaults,graph,character-method", "nodeDataDefaults,graph,missing-method", "nodeDataDefaults<-,graph,character,ANY-method", "nodeDataDefaults<-,graph,character-method", "nodeDataDefaults<-,graph,missing,list-method", "nodes,graph-method", "nodes<-,graph,character-method", "numEdges", "numEdges,graph-method", "numNodes", "numNodes,graph-method", "plot,graph,ANY-method", "plot,graph-method", "show,graph-method", "union,graph,graph-method", "updateGraph", "updateGraph,graph-method" ] }, { "page": "defunct", "title": "Defunct Functions in Package 'graph'", "topics": [ "buildRepDepGraph", "graph-defunct", "pkgInstOrder", "ugraphOld" ] }, { "page": "settings", "title": "Graphical parameters and other settings", "topics": [ "graph.par", "graph.par.get" ] }, { "page": "graph2SparseM", "title": "Coercion methods between graphs and sparse matrices", "topics": [ "graph2SparseM", "sparseM2Graph" ] }, { "page": "graphAM-class", "title": "Class \"graphAM\"", "topics": [ "addEdge,character,character,graphAM,missing-method", "addNode,character,graphAM,missing-method", "clearNode,character,graphAM-method", "coerce,graphAM,graphBAM-method", "coerce,graphAM,graphNEL-method", "coerce,graphAM,matrix-method", "coerce,matrix,graphAM-method", "edges,graphAM-method", "graphAM", "graphAM-class", "inEdges,character,graphAM-method", "inEdges,graphAM,missing-method", "inEdges,missing,graphAM-method", "initialize,graphAM-method", "isAdjacent,graphAM,character,character-method", "nodes,graphAM-method", "nodes<-,graphAM,character-method", "numEdges,graphAM-method", "numNodes,graphAM-method", "removeEdge,character,character,graphAM-method", "removeNode,character,graphAM-method" ] }, { "page": "graphBAM-class", "title": "EXPERIMENTAL class \"graphBAM\"", "topics": [ "addEdge,character,character,graphBAM,missing-method", "addEdge,character,character,graphBAM,numeric-method", "adj,graphBAM,character-method", "clearNode,character,graphBAM-method", "coerce,graphBAM,graphAM-method", "coerce,graphBAM,graphNEL-method", "coerce,graphBAM,matrix-method", "edgeData,graphBAM,character,character,character-method", "edgeData,graphBAM,character,missing,character-method", "edgeData,graphBAM,missing,character,character-method", "edgeData,graphBAM,missing,missing,character-method", "edgeData,graphBAM,missing,missing,missing-method", "edgeData<-,graphBAM,character,character,character,ANY-method", "edgeData<-,graphBAM,character,character,character-method", "edgeData<-,graphBAM,character,missing,character,ANY-method", "edgeData<-,graphBAM,character,missing,character-method", "edgeData<-,graphBAM,missing,character,character,ANY-method", "edgeData<-,graphBAM,missing,character,character-method", "edgeData<-,graphBAM,missing,missing,character,ANY-method", "edgeData<-,graphBAM,missing,missing,character-method", "edgeDataDefaults<-,graphBAM,character,ANY-method", "edgeDataDefaults<-,graphBAM,missing,list-method", "edgemode<-,graphBAM,character-method", "edges,graphBAM-method", "edgeWeights,graphBAM,character-method", "edgeWeights,graphBAM,missing-method", "edgeWeights,graphBAM,numeric-method", "edgeWeights,graphBAM-method", "extractFromTo,graphBAM-method", "graphBAM", "graphBAM-class", "graphIntersect", "graphIntersect,graphBAM,graphBAM-method", "graphUnion", "graphUnion,graphBAM,graphBAM-method", "inEdges,character,graphBAM-method", "initialize,graphBAM-method", "isAdjacent,graphBAM,character,character-method", "nodeData,graphBAM,character,character-method", "nodeData,graphBAM,character,missing-method", "nodeData,graphBAM,missing,character-method", "nodeData,graphBAM,missing,missing-method", "nodeData<-,graphBAM,character,character-method", "nodeData<-,graphBAM,missing,character-method", "nodeDataDefaults,graphBAM,character-method", "nodeDataDefaults,graphBAM,missing-method", "nodeDataDefaults<-,graphBAM,character,ANY-method", "nodeDataDefaults<-,graphBAM,missing,ANY-method", "nodeDataDefaults<-,graphBAM,missing,list-method", "nodes,graphBAM-method", "nodes<-,graphBAM,character-method", "numEdges,graphBAM-method", "numNodes,graphBAM-method", "removeEdge,character,character,graphBAM-method", "removeEdgesByWeight", "removeEdgesByWeight,graphBAM-method", "removeNode,character,graphBAM-method", "show,graphBAM-method", "ugraph,graphBAM-method" ] }, { "page": "graphExamples", "title": "A List Of Example Graphs", "topics": [ "graphExamples" ] }, { "page": "graphNEL-class", "title": "Class \"graphNEL\"", "topics": [ "addEdge,character,character,graphNEL,missing-method", "addEdge,character,character,graphNEL,numeric-method", "addNode,character,graphNEL-method", "adj,graphNEL,ANY-method", "clearNode,character,graphNEL-method", "coerce", "coerce,graphNEL,generalGraph-method", "coerce,graphNEL,graphAM-method", "coerce,graphNEL,graphBAM-method", "edgeL", "edgeL,graphNEL-method", "edges", "edges,graphNEL-method", "edgeWeights,graphNEL-method", "graphNEL", "graphNEL-class", "inEdges,character,graphNEL-method", "inEdges,graphNEL,missing-method", "inEdges,missing,graphNEL-method", "initialize", "initialize,graphNEL-method", "nodes", "nodes,graphNEL-method", "nodes<-", "nodes<-,graphNEL,character-method", "numNodes,graphNEL-method", "removeEdge,character,character,graphNEL-method", "removeNode,character,graphNEL-method", "toGXL,graphNEL-method" ] }, { "page": "inEdges", "title": "Generic Method inEdges", "topics": [ "inEdges" ] }, { "page": "IMCA", "title": "KEGG Integrin Mediated Cell Adhesion graph", "topics": [ "IMCA", "IMCAAttrs", "IMCAGraph", "integrinMediatedCellAdhesion" ] }, { "page": "isAdjacent-methods", "title": "Determine if nodes share an edge in a graph", "topics": [ "isAdjacent", "isAdjacent-methods" ] }, { "page": "isDirected-methods", "title": "Determine if a graph has directed or undirected edges", "topics": [ "isDirected", "isDirected-methods" ] }, { "page": "leaves", "title": "Find the leaves of a graph", "topics": [ "leaves", "leaves,graph-method" ] }, { "page": "listEdges", "title": "List the Edges of a Graph", "topics": [ "listEdges" ] }, { "page": "MAPKsig", "title": "A graph encoding parts of the MAPK signaling pathway", "topics": [ "MAPKsig" ] }, { "page": "mostEdges", "title": "Find the node in a graph with the greatest number of edges", "topics": [ "mostEdges" ] }, { "page": "multigraph", "title": "Class \"multiGraph\"", "topics": [ "edgemode,edgeSet-method", "edges,edgeSetAM-method", "edges,edgeSetNEL-method", "edges,multiGraph-method", "edgeSet-class", "edgeSetAM-class", "edgeSetNEL-class", "isDirected,edgeSet-method", "isDirected,multiGraph-method", "multiGraph-class", "nodes,edgeSetAM-method", "nodes,multiGraph-method", "numEdges,edgeSetAM-method", "numEdges,multiGraph-method", "numNodes,multiGraph-method", "show,edgeSet-method", "show,multiGraph-method" ] }, { "page": "MultiGraph-class", "title": "EXPERIMENTAL class \"MultiGraph\"", "topics": [ "edgeNames,MultiGraph-method", "edges,MultiGraph-method", "edgeSetIntersect0", "edgeSets", "edgeSets,MultiGraph-method", "edgeSetUnion0", "eweights", "extractFromTo", "extractFromTo,MultiGraph-method", "extractGraphAM", "extractGraphBAM", "graphIntersect,MultiGraph,MultiGraph-method", "graphUnion,MultiGraph,MultiGraph-method", "isDirected,DiEdgeSet-method", "isDirected,MultiGraph-method", "isDirected,UEdgeSet-method", "mgEdgeData", "mgEdgeData,MultiGraph,character,character,character,character-method", "mgEdgeData,MultiGraph,character,character,missing,character-method", "mgEdgeData,MultiGraph,character,missing,character,character-method", "mgEdgeData,MultiGraph,character,missing,missing,character-method", "mgEdgeData<-", "mgEdgeData<-,MultiGraph,character,character,character,character-method", "mgEdgeData<-,MultiGraph,character,character,missing,character-method", "mgEdgeData<-,MultiGraph,character,missing,character,character-method", "mgEdgeData<-,MultiGraph,character,missing,missing,character-method", "mgEdgeDataDefaults", "mgEdgeDataDefaults,MultiGraph,character,character-method", "mgEdgeDataDefaults,MultiGraph,character,missing-method", "mgEdgeDataDefaults<-", "mgEdgeDataDefaults<-,MultiGraph,character,character,ANY-method", "mgEdgeDataDefaults<-,MultiGraph,character,missing,list-method", "MultiGraph", "MultiGraph-class", "nodeData,MultiGraph,character,character-method", "nodeData,MultiGraph,character,missing-method", "nodeData,MultiGraph,missing,character-method", "nodeData,MultiGraph,missing,missing-method", "nodeData<-,MultiGraph,character,character-method", "nodeData<-,MultiGraph,missing,character-method", "nodeDataDefaults,MultiGraph,character-method", "nodeDataDefaults,MultiGraph,missing-method", "nodeDataDefaults<-,MultiGraph,character,ANY-method", "nodeDataDefaults<-,MultiGraph,missing,list-method", "nodes,MultiGraph-method", "numEdges,MGEdgeSet-method", "numEdges,MultiGraph-method", "numNodes,MultiGraph-method", "show,MultiGraph-method", "subsetEdgeSets", "ugraph,DiEdgeSet-method", "ugraph,MultiGraph-method", "ugraph,UEdgeSet-method" ] }, { "page": "nodeData-methods", "title": "Get and set attributes for the nodes of a graph object", "topics": [ "nodeData", "nodeData-methods", "nodeData<-", "nodeData<--methods" ] }, { "page": "nodeDataDefaults-methods", "title": "Get and set default attributes for the nodes of a graph", "topics": [ "nodeDataDefaults", "nodeDataDefaults-methods", "nodeDataDefaults<-", "nodeDataDefaults<--methods" ] }, { "page": "numNoEdges", "title": "Calculate the number of nodes that have an edge list of NULL", "topics": [ "numNoEdges" ] }, { "page": "pancrCaIni", "title": "A graph encoding parts of the pancreatic cancer initiation pathway", "topics": [ "pancrCaIni" ] }, { "page": "randomEGraph", "title": "Random Edge Graph", "topics": [ "randomEGraph" ] }, { "page": "randomGraph", "title": "Random Graph", "topics": [ "randomGraph" ] }, { "page": "randomNodeGraph", "title": "Generate Random Graph with Specified Degree Distribution", "topics": [ "randomNodeGraph" ] }, { "page": "removeEdge", "title": "removeEdge", "topics": [ "removeEdge" ] }, { "page": "removeNode", "title": "removeNode", "topics": [ "removeNode" ] }, { "page": "renderInfo-class", "title": "Class \"renderInfo\"", "topics": [ "edgeRenderInfo", "edgeRenderInfo<-", "graphRenderInfo", "graphRenderInfo<-", "nodeRenderInfo", "nodeRenderInfo<-", "parRenderInfo", "parRenderInfo<-", "renderInfo-class" ] }, { "page": "reverseEdgeDirections", "title": "Reverse the edges of a directed graph", "topics": [ "reverseEdgeDirections" ] }, { "page": "simpleEdge-class", "title": "Class \"simpleEdge\".", "topics": [ "simpleEdge-class" ] }, { "page": "standardLabeling", "title": "Standard labeling of edges with integers", "topics": [ "ftM2int", "int2ftM" ] }, { "page": "subGraph", "title": "Create a Subgraph", 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