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A B C D E F G H I J L M N P R S T U V W misc
| acc | Methods for Accessibility Lists |
| acc,clusterGraph,character-method | Methods for Accessibility Lists |
| acc,clusterGraph-method | Methods for Accessibility Lists |
| acc,graph,character-method | Methods for Accessibility Lists |
| acc,graph-method | Methods for Accessibility Lists |
| acc-methods | Methods for Accessibility Lists |
| addEdge | addEdge |
| addEdge,character,character,graphNEL,numeric-method | Class "graphNEL" |
| addNode | addNode |
| addNode,character,distGraph,list-method | addNode |
| addNode,character,graphNEL,list-method | addNode |
| addNode,character,graphNEL,missing-method | addNode |
| addNode,character,graphNEL-method | Class "graphNEL" |
| adj | Methods for finding the adjacency list for selected nodes. |
| adj,clusterGraph-method | Class "clusterGraph" |
| adj,distGraph-method | Class "distGraph" |
| adj,graphNEL-method | Class "graphNEL" |
| adj-methods | Methods for finding the adjacency list for selected nodes. |
| aM2bpG | Coercing matrices to graphs |
| apopAttrs | KEGG apoptosis pathway graph |
| apopGraph | KEGG apoptosis pathway graph |
| apopLocusLink | KEGG apoptosis pathway graph |
| aveNumEdges | Calculate the average number of edges in a graph |
| biocRepos | A graph representing the Bioconductor package repository |
| bNode | Class "gEdge" |
| bNode,gEdge-method | Class "gEdge" |
| 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 |
| clearNode,character,graphNEL-method | Class "graphNEL" |
| clusterGraph-class | Class "clusterGraph" |
| coerce | Class "graphNEL" |
| coerce,generalGraph-method | Class "generalGraph" ~~~ |
| coerce,graphNEL,generalGraph-method | Class "graphNEL" |
| coerce,graphNEL,matrix-method | Coercing matrices to graphs |
| coerce,matrix,graphNEL-method | Coercing matrices to graphs |
| combineNodes | combineNodes |
| combineNodes,character,graphNEL,character-method | Class "graphNEL" |
| complement | Class "graph" |
| complement,graph-method | Class "graph" |
| connComp | Class "graph" |
| connComp,clusterGraph-method | Class "clusterGraph" |
| connComp,graph-method | Class "graph" |
| connection-class | Methods for GXL manipulations in package graph |
| contents | Class "hashtable" |
| contents,hashtable,ANY-method | Class "hashtable" |
| contents,hashtable-method | Class "hashtable" |
| degree | Class "graph" |
| degree,graph,ANY-method | Class "graph" |
| degree,graph,missing-method | Class "graph" |
| DFS | Depth First Search |
| DFS,graph,character-method | Depth First Search |
| dfs,graph-method | Class "graph" |
| Dist | Class "distGraph" |
| Dist,distGraph-method | Class "distGraph" |
| distGraph-class | Class "distGraph" |
| dumpGXL | Methods for GXL manipulations in package graph |
| dumpGXL,connection-method | Methods for GXL manipulations in package graph |
| dumpGXL-methods | Methods for GXL manipulations in package graph |
| duplicatedEdges | duplicatedEdges |
| edgeID | Class "gEdge" |
| edgeID,gEdge-method | Class "gEdge" |
| edgeL | Class "graphNEL" |
| edgeL,graphNEL-method | Class "graphNEL" |
| edgeMatrix | Compute an Edge Matrix or weight vector for a Graph |
| edgeMatrix,clusterGraph-method | Compute an Edge Matrix or weight vector for a Graph |
| edgeMatrix,distGraph-method | Compute an Edge Matrix or weight vector for a Graph |
| edgeMatrix,graphNEL-method | Compute an Edge Matrix or weight vector for a Graph |
| edgemode | Class "graph" |
| edgemode,graph-method | Class "graph" |
| edgemode<-,graph,character-method | Class "graph" |
| edgeOrder | Class "gNode" |
| edgeOrder,gNode-method | Class "gNode" |
| edges | Class "graphNEL" |
| edges,clusterGraph,character-method | Class "clusterGraph" |
| edges,clusterGraph,missing-method | Class "clusterGraph" |
| edges,distGraph,character-method | Class "distGraph" |
| edges,distGraph,missing-method | Class "distGraph" |
| edges,graphNEL,character-method | Class "graphNEL" |
| edges,graphNEL,missing-method | Class "graphNEL" |
| edgeWeights | Retrieve the edge weights for specified indices. |
| edgeWeights,clusterGraph-method | Class "clusterGraph" |
| edgeWeights,distGraph-method | Class "distGraph" |
| edgeWeights,graphNEL-method | Class "graphNEL" |
| eNode | Class "gEdge" |
| eNode,gEdge-method | Class "gEdge" |
| eWV | Compute an Edge Matrix or weight vector for a Graph |
| file-class | Methods for GXL manipulations in package graph |
| fromEdges | Class "gNode" |
| fromEdges,gNode-method | Class "gNode" |
| fromEdges<-,gNode-method | Class "gNode" |
| fromGXL | Methods for GXL manipulations in package graph |
| fromGXL,connection-method | Methods for GXL manipulations in package graph |
| fromGXL-methods | Methods for GXL manipulations in package graph |
| ftM2adjM | Coercing matrices to graphs |
| gEdge-class | Class "gEdge" |
| generalGraph-class | Class "generalGraph" ~~~ |
| gNode-class | Class "gNode" |
| graph-class | Class "graph" |
| graph2SparseM | Coercion methods between graphs and sparse matrices |
| graphExamples | A List Of Example Graphs |
| graphID-class | Unique Graph Identifications |
| graphNEL-class | Class "graphNEL" |
| GXL | Methods for GXL manipulations in package graph |
| gxlTreeNEL | Methods for GXL manipulations in package graph |
| hash | Class "hashtable" |
| hash,ANY,ANY,hashtable-method | Class "hashtable" |
| hashtable-class | Class "hashtable" |
| idenv | Functions to associate identifiers with graph components. |
| IMCA | KEGG Integrin Mediated Cell Adhesion graph |
| IMCAAttrs | KEGG Integrin Mediated Cell Adhesion graph |
| IMCAGraph | KEGG Integrin Mediated Cell Adhesion graph |
| IMCALocusLink | KEGG Integrin Mediated Cell Adhesion graph |
| inEdges | inEdges |
| inEdges,character,graphNEL-method | Class "graphNEL" |
| inEdges,graphNEL,missing-method | inEdges |
| inEdges,missing,graphNEL-method | Class "graphNEL" |
| initialize | Class "graphNEL" |
| initialize,generalGraph-method | Class "generalGraph" ~~~ |
| initialize,graphNEL-method | Class "graphNEL" |
| initialize,hashtable-method | Class "hashtable" |
| intersection | Class "graph" |
| intersection,graph,graph-method | Class "graph" |
| isConnected | Class "graph" |
| isConnected,graph-method | Class "graph" |
| join | Class "graph" |
| join,graph,graph-method | Class "graph" |
| label | Class "gNode" |
| label,gNode-method | Class "gNode" |
| listEdges | List the Edges of a Graph |
| mostEdges | Find the node in a graph with the greatest number of edges |
| NELhandler | Methods for GXL manipulations in package graph |
| newID | Functions to associate identifiers with graph components. |
| nodeID | Class "gNode" |
| nodeID,gNode-method | Class "gNode" |
| nodes | Class "graphNEL" |
| nodes,clusterGraph-method | Class "clusterGraph" |
| nodes,distGraph-method | Class "distGraph" |
| nodes,graphNEL-method | Class "graphNEL" |
| nodes<-,graphNEL,character-method | Class "graphNEL" |
| nodeType | Class "gNode" |
| nodeType,gNode-method | Class "gNode" |
| nullgraphID | Functions to associate identifiers with graph components. |
| numEdges | Calculate the number of edges in a graph |
| numNodes | Class "graph" |
| numNodes,clusterGraph-method | Class "clusterGraph" |
| numNodes,distGraph-method | Class "distGraph" |
| numNodes,graph-method | Class "graph" |
| numNodes,graphNEL-method | Class "graphNEL" |
| numNoEdges | Calculate the number of nodes that have an edge list of NULL |
| pathWeights | Compute an Edge Matrix or weight vector for a Graph |
| pkgInstOrder | Functionality to manage repository dependency graphs |
| randomEGraph | Random Edge Graph |
| randomGraph | Random Graph |
| randomNodeGraph | Generate a Graph with specified degree distribution. |
| removeEdge | removeEdge |
| removeEdge,character,character,graphNEL-method | Class "graphNEL" |
| removeNode | removeNode |
| removeNode,character,graphNEL-method | Class "graphNEL" |
| show | Class "graphNEL" |
| show,clusterGraph-method | Class "clusterGraph" |
| show,distGraph-method | Class "distGraph" |
| show,graphNEL-method | Class "graphNEL" |
| simpleEdge-class | Class "simpleEdge". |
| sparseM2Graph | Coercion methods between graphs and sparse matrices |
| startids | Functions to associate identifiers with graph components. |
| subGraph | Create a Subgraph |
| subGraph,character,clusterGraph-method | Create a Subgraph |
| subGraph,character,distGraph-method | Create a Subgraph |
| subGraph,character,graphNEL-method | Create a Subgraph |
| threshold | Class "distGraph" |
| threshold,distGraph-method | Class "distGraph" |
| toEdges | Class "gNode" |
| toEdges,gNode-method | Class "gNode" |
| toEdges<-,gNode-method | Class "gNode" |
| toGXL | Methods for GXL manipulations in package graph |
| toGXL,graphNEL-method | Class "graphNEL" |
| toGXL-methods | Methods for GXL manipulations in package graph |
| ugraph | Underlying Graph |
| union | Class "graph" |
| union,graph,graph-method | Class "graph" |
| validateGXL | Methods for GXL manipulations in package graph |
| validateGXL,connection-method | Methods for GXL manipulations in package graph |
| validGraph | Test whether graph object is valid |
| write.tlp | Write a graph object in a file in the Tulip format |
| [.dist | Class "distGraph" |