DFS Depth First Search MAPKsig A graph encoding parts of the MAPK signaling pathway aM2bpG Coercions between matrix and graph representations acc-methods Methods for Accessibility Lists addEdge addEdge addNode addNode adj-methods Methods for finding the adjacency list for selected nodes. apopGraph KEGG apoptosis pathway graph attrData-class Class "attrData" attrDataItem-methods Get and set attributes values for items in an attrData object attrDefaults-methods Get and set the default attributes of an attrData object aveNumEdges Calculate the average number of edges in a graph biocRepos A graph representing the Bioconductor package repository boundary Returns the Boundary between a Graph and a SubGraph buildRepDepGraph Functionality to manage repository dependency graphs calcProb Calculate the hypergeometric probability of the subgraph's number of edges. calcSumProb Calculate the probability that a subgraph has an unusual number of edges. clearNode clearNode clusterGraph-class Class "clusterGraph" clusteringCoefficient Clustering coefficient of a graph combineNodes combineNodes distGraph-class Class "distGraph" duplicatedEdges duplicatedEdges edgeData-methods Get and set attributes for the edges of a graph object edgeDataDefaults-methods Get and set default attributes for the edges of a graph edgeMatrix Compute an Edge Matrix or weight vector for a Graph edgeWeights Retrieve the edge weights of a graph fromGXL-methods Methods for GXL manipulations in package graph ftM2int Standard labeling of edges with integers graph-class Class "graph" graph.par Graphical parameters and other settings graph2SparseM Coercion methods between graphs and sparse matrices graphAM-class Class "graphAM" graphExamples A List Of Example Graphs graphNEL-class Class "graphNEL" graphRendering How to render a graph inEdges Generic Method inEdges integrinMediatedCellAdhesion KEGG Integrin Mediated Cell Adhesion graph isAdjacent-methods Determine if nodes share an edge in a graph isDirected-methods Determine if a graph has directed or undirected edges leaves Find the leaves of a graph listEdges List the Edges of a Graph mostEdges Find the node in a graph with the greatest number of edges multiGraph-class Class "multiGraph" nodeData-methods Get and set attributes for the nodes of a graph object nodeDataDefaults-methods Get and set default attributes for the nodes of a graph numNoEdges Calculate the number of nodes that have an edge list of NULL pancrCaIni A graph encoding parts of the pancreatic cancer initiation pathway randomEGraph Random Edge Graph randomGraph Random Graph randomNodeGraph Generate Random Graph with Specified Degree Distribution removeEdge removeEdge removeNode removeNode renderInfo-class Class "renderInfo" reverseEdgeDirections Reverse the edges of a directed graph simpleEdge-class Class "simpleEdge". subGraph Create a Subgraph toDotR Methods for Function toDotR, using R to generate a dot serialization ugraph Underlying Graph validGraph Test whether graph object is valid write.tlp Write a graph object in a file in the Tulip format