Entry: DFS
Aliases: DFS DFS,graph,character-method
Keywords: manip
Description: Depth First Search
URL: ../../../library/graph/html/DFS.html

Entry: integrinMediatedCellAdhesion
Aliases: IMCA IMCAAttrs IMCAGraph integrinMediatedCellAdhesion
Keywords: datasets
Description: KEGG Integrin Mediated Cell Adhesion graph
URL: ../../../library/graph/html/IMCA.html

Entry: acc-methods
Aliases: acc-methods acc,graph-method acc,clusterGraph-method acc acc,graph,character-method acc,clusterGraph,character-method
Keywords: methods
Description: Methods for Accessibility Lists
URL: ../../../library/graph/html/acc-methods.html

Entry: addEdge
Aliases: addEdge
Keywords: manip
Description: addEdge
URL: ../../../library/graph/html/addEdge.html

Entry: addNode
Aliases: addNode addNode,character,graphNEL,missing-method addNode,character,graphNEL,list-method addNode,character,distGraph,list-method
Keywords: manip
Description: addNode
URL: ../../../library/graph/html/addNode.html

Entry: adj-methods
Aliases: adj adj-methods
Keywords: methods
Description: Methods for finding the adjacency list for selected nodes.
URL: ../../../library/graph/html/adj-methods.html

Entry: apoptosisGraph
Aliases: apopGraph apopAttrs apopLocusLink
Keywords: datasets
Description: KEGG apoptosis pathway graph
URL: ../../../library/graph/html/apoptosisGraph.html

Entry: asGraphProperty
Aliases: asGraphProperty asGraphProperty-methods asGraphProperty,list,missing-method asGraphProperty,numeric,missing-method asGraphProperty,list,logical-method asGraphProperty,numeric,logical-method
Keywords: methods
Description: Generic for converting input to graph property list
URL: ../../../library/graph/html/asGraphProperty.html

Entry: attrData-class
Aliases: attrData-class attrDataItem<-,attrData,character,character-method attrDataItem,attrData,character,missing-method attrDataItem,attrData,character,character-method attrDefaults<-,attrData,character,ANY-method attrDefaults<-,attrData,missing,list-method attrDefaults,attrData,missing-method attrDefaults,attrData,character-method initialize,attrData-method removeAttrDataItem<- removeAttrDataItem<-,attrData,character,NULL-method
Keywords: classes
Description: Class "attrData"
URL: ../../../library/graph/html/attrData-class.html

Entry: attrDataItem-methods
Aliases: attrDataItem-methods attrDataItem<--methods attrDataItem attrDataItem<-
Keywords: methods
Description: Get and set attributes values for items in an attrData object
URL: ../../../library/graph/html/attrDataItem-methods.html

Entry: attrDefaults-methods
Aliases: attrDefaults-methods attrDefaults<--methods attrDefaults attrDefaults<-
Keywords: methods
Description: Get and set the default attributes of an attrData object
URL: ../../../library/graph/html/attrDefaults-methods.html

Entry: aveNumEdges
Aliases: aveNumEdges
Keywords: manip
Description: Calculate the average number of edges in a graph
URL: ../../../library/graph/html/aveNumEdges.html

Entry: biocRepos
Aliases: biocRepos
Keywords: datasets
Description: A graph representing the Bioconductor package repository
URL: ../../../library/graph/html/biocRepos.html

Entry: boundary
Aliases: boundary
Keywords: manip
Description: Returns the Boundary between a Graph and a SubGraph
URL: ../../../library/graph/html/boundary.html

Entry: buildRepDepGraph
Aliases: buildRepDepGraph pkgInstOrder
Keywords: graphs
Description: Functionality to manage repository dependency graphs
URL: ../../../library/graph/html/buildRepDepGraph.html

Entry: calcProb
Aliases: calcProb
Keywords: manip
Description: Calculate the hypergeometric probability of the subgraph's number of edges.
URL: ../../../library/graph/html/calcProb.html

Entry: calcSumProb
Aliases: calcSumProb
Keywords: manip
Description: Calculate the probability that a subgraph has an unusual number of edges.
URL: ../../../library/graph/html/calcSumProb.html

Entry: clearNode
Aliases: clearNode
Keywords: manip
Description: clearNode
URL: ../../../library/graph/html/clearNode.html

Entry: clusterGraph-class
Aliases: clusterGraph-class clusterGraph-class adj,clusterGraph-method connComp,clusterGraph-method edges,clusterGraph,missing-method edges,clusterGraph,character-method edgeWeights,clusterGraph-method nodes,clusterGraph-method nodes<-,clusterGraph,character-method numNodes,clusterGraph-method show,clusterGraph-method
Keywords: classes
Description: Class "clusterGraph"
URL: ../../../library/graph/html/clusterGraph-class.html

Entry: clusteringCoefficient-methods
Aliases: clusteringCoefficient clusteringCoefficient,graph-method clusteringCoefficient,graph
Keywords: methods
Description: Clustering coefficient of a graph
URL: ../../../library/graph/html/clusteringCoefficient-methods.html

Entry: combineNodes
Aliases: combineNodes
Keywords: manip
Description: combineNodes
URL: ../../../library/graph/html/combineNodes.html

Entry: distGraph-class
Aliases: distGraph-class threshold Dist [.dist distGraph-class adj,distGraph-method Dist,distGraph-method edges,distGraph,missing-method edges,distGraph,character-method nodes,distGraph-method numNodes,distGraph-method show,distGraph-method threshold,distGraph-method edgeWeights,distGraph-method initialize,distGraph-method
Keywords: classes
Description: Class "distGraph"
URL: ../../../library/graph/html/distGraph-class.html

Entry: duplicatedEdges
Aliases: duplicatedEdges
Keywords: manip
Description: duplicatedEdges
URL: ../../../library/graph/html/duplicatedEdges.html

Entry: edgeData-methods
Aliases: edgeData-methods edgeData<--methods edgeData edgeData<-
Keywords: methods
Description: Get and set attributes for the edges of a graph object
URL: ../../../library/graph/html/edgeData-methods.html

Entry: edgeDataDefaults-methods
Aliases: edgeDataDefaults-methods edgeDataDefaults<--methods edgeDataDefaults edgeDataDefaults<-
Keywords: methods
Description: Get and set default attributes for the edges of a graph
URL: ../../../library/graph/html/edgeDataDefaults-methods.html

Entry: edgeMatrix
Aliases: edgeMatrix eWV pathWeights edgeMatrix,graphNEL-method edgeMatrix,clusterGraph-method edgeMatrix,distGraph-method
Keywords: manip
Description: Compute an Edge Matrix or weight vector for a Graph
URL: ../../../library/graph/html/edgeMatrix.html

Entry: edgeWeights
Aliases: edgeWeights
Keywords: manip
Description: Retrieve the edge weights for specified indices.
URL: ../../../library/graph/html/edgeWeights.html

Entry: fromGXL-methods
Aliases: fromGXL-methods toGXL-methods GXL dumpGXL-methods dumpGXL fromGXL gxlTreeNEL NELhandler toGXL validateGXL connection-class file-class dumpGXL,connection-method fromGXL,connection-method validateGXL,connection-method
Keywords: methods models
Description: Methods for GXL manipulations in package graph
URL: ../../../library/graph/html/fromGXL-methods.html

Entry: gEdge-class
Aliases: gEdge-class edgeID bNode eNode edgeID,gEdge-method bNode,gEdge-method eNode,gEdge-method idstring,gEdge-method initialize,gEdge-method
Keywords: classes
Description: Class "gEdge"
URL: ../../../library/graph/html/gEdge-class.html

Entry: gNode-class
Aliases: gNode-class edgeOrder edgeOrder,gNode-method fromEdges fromEdges,gNode-method fromEdges<- fromEdges<-,gNode-method toEdges toEdges,gNode-method toEdges<- toEdges<-,gNode-method label label,gNode-method nodeID nodeID,gNode-method nodeType nodeType,gNode-method initialize,gNode-method idstring,gNode-method
Keywords: classes
Description: Class "gNode"
URL: ../../../library/graph/html/gNode-class.html

Entry: generalGraph-class
Aliases: generalGraph-class coerce,generalGraph-method initialize,generalGraph-method
Keywords: classes
Description: Class "generalGraph" ~~~
URL: ../../../library/graph/html/generalGraph-class.html

Entry: graph-class
Aliases: graph-class complement complement,graph-method connComp connComp,graph-method degree degree,graph,missing-method degree,graph,ANY-method dfs,graph-method edgeDataDefaults<-,graph,missing,list-method edgeDataDefaults<-,graph,character-method edgeDataDefaults,graph,missing-method edgeDataDefaults,graph,character-method edgeData<-,graph,character,character,character-method edgeData<-,graph,character,missing,character-method edgeData<-,graph,missing,character,character-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 edgemode edgemode<- edgemode,graph-method edgemode<-,graph,character-method edgeNames edgeNames,graph-method edgeL,graph-method edgeWeights,graph,character-method edgeWeights,graph,numeric-method edgeWeights,graph,missing-method intersection intersection,graph,graph-method intersection2 intersection2,graph,graph-method intersection3 intersection3,graph,graph-method isAdjacent,graph,character,character-method isConnected isConnected,graph-method isDirected,graph-method join join,graph,graph-method nodeDataDefaults<-,graph,missing,list-method nodeDataDefaults<-,graph,character-method nodeDataDefaults,graph,missing-method nodeDataDefaults,graph,character-method nodeData<-,graph,character,character-method nodeData<-,graph,missing,character-method nodeData,graph,character,character-method nodeData,graph,character,missing-method nodeData,graph,missing,character-method nodeData,graph,missing,missing-method numEdges numEdges,graph-method numNodes numNodes,graph-method show show,graph-method union union,graph,graph-method
Keywords: graphs classes
Description: Class "graph"
URL: ../../../library/graph/html/graph-class.html

Entry: graph2SparseM
Aliases: graph2SparseM sparseM2Graph
Keywords: manip
Description: Coercion methods between graphs and sparse matrices
URL: ../../../library/graph/html/graph2SparseM.html

Entry: graphAM-class
Aliases: graphAM-class addEdge,character,character,graphAM,missing-method addNode,character,graphAM,missing-method clearNode,character,graphAM-method coerce,graphAM,graphNEL-method coerce,graphAM,matrix-method coerce,matrix,graphAM-method edges,graphAM,missing-method edges,graphAM,character-method initialize,graphAM-method inEdges,missing,graphAM-method inEdges,character,graphAM-method inEdges,graphAM,missing-method isAdjacent,graphAM,character,character-method nodes<-,graphAM,character-method nodes,graphAM-method numEdges,graphAM-method numNodes,graphAM-method removeEdge,character,character,graphAM-method removeNode,character,graphAM-method
Keywords: graphs classes
Description: Class "graphAM"
URL: ../../../library/graph/html/graphAM-class.html

Entry: graphExamples
Aliases: graphExamples
Keywords: datasets
Description: A List Of Example Graphs
URL: ../../../library/graph/html/graphExamples.html

Entry: graphH-class
Aliases: graphH-class getNodes idstring degree,graphH,missing-method degree,graphH,character-method edges,graphH,missing-method edges,graphH,character-method getNodes,graphH,missing-method getNodes,graphH,character-method idstring,graphH-method initialize,graphH-method nodes,graphH-method nodes<-,graphH,character-method
Keywords: classes
Description: Class "graphH"
URL: ../../../library/graph/html/graphH-class.html

Entry: graphID-class
Aliases: graphID-class
Keywords: classes
Description: Unique Graph Identifications
URL: ../../../library/graph/html/graphID-class.html

Entry: graphNEL-class
Aliases: graphNEL-class coerce edgeL edges edges initialize nodes<- nodes addEdge,character,character,graphNEL,numeric-method addEdge,character,character,graphNEL,missing-method addNode,character,graphNEL-method adj,graphNEL-method clearNode,character,graphNEL-method coerce,graphNEL,generalGraph-method coerce,graphNEL,graphAM-method combineNodes,character,graphNEL,character-method edgeL,graphNEL-method edges,graphNEL,missing-method edges,graphNEL,character-method edgeWeights,graphNEL-method inEdges,graphNEL,missing-method inEdges,missing,graphNEL-method inEdges,character,graphNEL-method initialize,graphNEL-method nodes<-,graphNEL,character-method nodes,graphNEL-method numNodes,graphNEL-method removeEdge,character,character,graphNEL-method removeNode,character,graphNEL-method toGXL,graphNEL-method
Keywords: classes
Description: Class "graphNEL"
URL: ../../../library/graph/html/graphNEL-class.html

Entry: hashtable-class
Aliases: hashtable-class hash contents hash,ANY,ANY,hashtable-method contents,hashtable,ANY-method contents,hashtable-method initialize,hashtable-method
Keywords: classes
Description: Class "hashtable"
URL: ../../../library/graph/html/hashtable-class.html

Entry: hashtable
Aliases: hashtable
Keywords: environment
Description: Create a hashtable
URL: ../../../library/graph/html/hashtable.html

Entry: inEdges
Aliases: inEdges
Keywords: manip
Description: Generic Method inEdges
URL: ../../../library/graph/html/inEdges.html

Entry: internal
Aliases: nullgraphID
Keywords: internal
Description: Variables used for internal purposes
URL: ../../../library/graph/html/internal.html

Entry: isAdjacent-methods
Aliases: isAdjacent-methods isAdjacent
Keywords: methods
Description: Determine if nodes share an edge in a graph
URL: ../../../library/graph/html/isAdjacent-methods.html

Entry: isDirected-methods
Aliases: isDirected-methods isDirected
Keywords: methods
Description: Determine if a graph has directed or undirected edges
URL: ../../../library/graph/html/isDirected-methods.html

Entry: listEdges
Aliases: listEdges
Keywords: manip
Description: List the Edges of a Graph
URL: ../../../library/graph/html/listEdges.html

Entry: Coercions between matrix and graph representations
Aliases: aM2bpG ftM2adjM ftM2graphNEL coerce,matrix,graphNEL-method coerce,graphNEL,matrix-method
Keywords: graphs
Description: Coercions between matrix and graph representations
URL: ../../../library/graph/html/matrix2Graph.html

Entry: mostEdges
Aliases: mostEdges
Keywords: manip
Description: Find the node in a graph with the greatest number of edges
URL: ../../../library/graph/html/mostEdges.html

Entry: nodeData-methods
Aliases: nodeData-methods nodeData<--methods nodeData nodeData<-
Keywords: methods
Description: Get and set attributes for the nodes of a graph object
URL: ../../../library/graph/html/nodeData-methods.html

Entry: nodeDataDefaults-methods
Aliases: nodeDataDefaults-methods nodeDataDefaults<--methods nodeDataDefaults nodeDataDefaults<-
Keywords: methods
Description: Get and set default attributes for the nodes of a graph
URL: ../../../library/graph/html/nodeDataDefaults-methods.html

Entry: numNoEdges
Aliases: numNoEdges
Keywords: manip
Description: Calculate the number of nodes that have an edge list of NULL
URL: ../../../library/graph/html/numNoEdges.html

Entry: propertyHolder-class
Aliases: propertyHolder-class property property<- property,propertyHolder,character-method property<-,propertyHolder,character-method
Keywords: classes
Description: Class "propertyHolder"
URL: ../../../library/graph/html/propertyHolder-class.html

Entry: randomEGraph
Aliases: randomEGraph
Keywords: manip
Description: Random Edge Graph
URL: ../../../library/graph/html/randomEGraph.html

Entry: randomGraph
Aliases: randomGraph
Keywords: graphs
Description: Random Graph
URL: ../../../library/graph/html/randomGraph.html

Entry: randomNodeGraph
Aliases: randomNodeGraph
Keywords: graphs manip
Description: Generate Random Graph with Specified Degree Distribution
URL: ../../../library/graph/html/randomNodeGraph.html

Entry: removeEdge
Aliases: removeEdge
Keywords: manip
Description: removeEdge
URL: ../../../library/graph/html/removeEdge.html

Entry: removeNode
Aliases: removeNode
Keywords: manip
Description: removeNode
URL: ../../../library/graph/html/removeNode.html

Entry: simpleEdge-class
Aliases: simpleEdge-class
Keywords: classes
Description: Class "simpleEdge".
URL: ../../../library/graph/html/simpleEdge-class.html

Entry: Standard labeling of edges with integers
Aliases: ftM2int int2ftM
Keywords: graphs
Description: Standard labeling of edges with integers
URL: ../../../library/graph/html/standardLabeling.html

Entry: subGraph
Aliases: subGraph subGraph,character,graphNEL-method subGraph,character,clusterGraph-method subGraph,character,distGraph-method
Keywords: manip
Description: Create a Subgraph
URL: ../../../library/graph/html/subGraph.html

Entry: toDotR-methods
Aliases: toDotR toDotR,graphNEL,character,list,list-method toDotR,graphNEL,character,missing,missing-method toDotR,graphNEL,character,missing,list-method toDotR,graphNEL,missing,missing,missing-method toDotR,graphNEL,missing,missing,list-method toDotR,graphNEL,missing,character,missing-method toDotR,graphNEL,missing,list,list-method toDotR,graphNEL,missing,list,missing-method
Keywords: methods
Description: Methods for Function toDotR, using R to generate a dot serialization
URL: ../../../library/graph/html/toDotR-methods.html

Entry: ugraph
Aliases: ugraph
Keywords: manip
Description: Underlying Graph
URL: ../../../library/graph/html/ugraph.html

Entry: validGraph
Aliases: validGraph
Keywords: manip
Description: Test whether graph object is valid
URL: ../../../library/graph/html/validGraph.html

Entry: write.tlp
Aliases: write.tlp
Keywords: manip
Description: Write a graph object in a file in the Tulip format
URL: ../../../library/graph/html/write.tlp.html
