graph: A package to handle graph data structures
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Documentation for package ‘graph’ version 1.87.0
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A B C D E F G I J L M N P R S T U V W misc
-- A --
| acc | Methods for Accessibility Lists |
| acc-method | Methods for Accessibility Lists |
| acc-methods | Methods for Accessibility Lists |
| addEdge | addEdge |
| addEdge-method | Class "graphAM" |
| addEdge-method | EXPERIMENTAL class "graphBAM" |
| addEdge-method | Class "graphNEL" |
| addNode | addNode |
| addNode-method | addNode |
| addNode-method | Class "graphAM" |
| addNode-method | Class "graphNEL" |
| adj | Methods for finding the adjacency list for selected nodes. |
| adj-method | Class "clusterGraph" |
| adj-method | Class "distGraph" |
| adj-method | EXPERIMENTAL class "graphBAM" |
| adj-method | Class "graphNEL" |
| adj-methods | Methods for finding the adjacency list for selected nodes. |
| adjacencyMatrix | Compute an Adjacency Matrix for a graphBAM object |
| adjacencyMatrix-method | Compute an Adjacency Matrix for a graphBAM object |
| aM2bpG | Coercions between matrix and graph representations |
| apopAttrs | KEGG apoptosis pathway graph |
| apopGraph | KEGG apoptosis pathway graph |
| apopLocusLink | KEGG apoptosis pathway graph |
| attrData-class | Class "attrData" |
| attrDataItem | Get and set attributes values for items in an attrData object |
| attrDataItem-method | Class "attrData" |
| attrDataItem-methods | Get and set attributes values for items in an attrData object |
| attrDataItem<- | Get and set attributes values for items in an attrData object |
| attrDataItem<--method | Class "attrData" |
| attrDataItem<--methods | Get and set attributes values for items in an attrData object |
| attrDefaults | Get and set the default attributes of an attrData object |
| attrDefaults-method | Class "attrData" |
| attrDefaults-methods | Get and set the default attributes of an attrData object |
| attrDefaults<- | Get and set the default attributes of an attrData object |
| attrDefaults<--method | Class "attrData" |
| attrDefaults<--methods | Get and set the default attributes of an attrData object |
| aveNumEdges | Calculate the average number of edges in a graph |
-- B --
| biocRepos | A graph representing the Bioconductor package repository |
| boundary | Returns the Boundary between a Graph and a SubGraph |
| buildRepDepGraph | Defunct Functions in Package 'graph' |
-- C --
| 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-method | Class "graphAM" |
| clearNode-method | EXPERIMENTAL class "graphBAM" |
| clearNode-method | Class "graphNEL" |
| clusterGraph-class | Class "clusterGraph" |
| clusteringCoefficient | Clustering coefficient of a graph |
| clusteringCoefficient,graph | Clustering coefficient of a graph |
| clusteringCoefficient-method | Clustering coefficient of a graph |
| coerce | Class "graphNEL" |
| coerce-method | Class "clusterGraph" |
| coerce-method | Class "graphAM" |
| coerce-method | EXPERIMENTAL class "graphBAM" |
| coerce-method | Class "graphNEL" |
| coerce-method | Coercions between matrix and graph representations |
| combineNodes | combineNodes |
| combineNodes-method | combineNodes |
| complement | Class "graph" |
| complement-method | Class "graph" |
| connComp | Class "graph" |
| connComp-method | Class "clusterGraph" |
| connComp-method | Class "graph" |
-- D --
| degree | Class "graph" |
| degree-method | Class "graph" |
| DFS | Depth First Search |
| DFS-method | Depth First Search |
| dfs-method | Class "graph" |
| Dist | Class "distGraph" |
| Dist-method | Class "distGraph" |
| distGraph-class | Class "distGraph" |
| dumpGXL | Methods for GXL manipulations in package graph |
| dumpGXL-method | Methods for GXL manipulations in package graph |
| dumpGXL-methods | Methods for GXL manipulations in package graph |
| duplicatedEdges | duplicatedEdges |
-- E --
| edgeData | Get and set attributes for the edges of a graph object |
| edgeData-method | Class "graph" |
| edgeData-method | EXPERIMENTAL class "graphBAM" |
| edgeData-methods | Get and set attributes for the edges of a graph object |
| edgeData<- | Get and set attributes for the edges of a graph object |
| edgeData<--method | Class "graph" |
| edgeData<--method | EXPERIMENTAL class "graphBAM" |
| edgeData<--methods | Get and set attributes for the edges of a graph object |
| edgeDataDefaults | Get and set default attributes for the edges of a graph |
| edgeDataDefaults-method | Class "graph" |
| edgeDataDefaults-methods | Get and set default attributes for the edges of a graph |
| edgeDataDefaults<- | Get and set default attributes for the edges of a graph |
| edgeDataDefaults<--method | Class "graph" |
| edgeDataDefaults<--method | EXPERIMENTAL class "graphBAM" |
| edgeDataDefaults<--methods | Get and set default attributes for the edges of a graph |
| edgeL | Class "graphNEL" |
| edgeL-method | Class "clusterGraph" |
| edgeL-method | Class "distGraph" |
| edgeL-method | Class "graph" |
| edgeL-method | Class "graphNEL" |
| edgeMatrix | Compute an Edge Matrix or weight vector for a Graph |
| edgeMatrix-method | Compute an Edge Matrix or weight vector for a Graph |
| edgemode | Class "graph" |
| edgemode-method | Class "graph" |
| edgemode-method | Class "multiGraph" |
| edgemode<- | Class "graph" |
| edgemode<--method | Class "graph" |
| edgemode<--method | EXPERIMENTAL class "graphBAM" |
| edgeNames | Class "graph" |
| edgeNames-method | EXPERIMENTAL class "MultiGraph" |
| edgeNames-method | Class "graph" |
| edgeRenderInfo | Class "renderInfo" |
| edgeRenderInfo<- | Class "renderInfo" |
| edges | Class "graphNEL" |
| edges-method | EXPERIMENTAL class "MultiGraph" |
| edges-method | Class "clusterGraph" |
| edges-method | Class "distGraph" |
| edges-method | Class "graphAM" |
| edges-method | EXPERIMENTAL class "graphBAM" |
| edges-method | Class "graphNEL" |
| edges-method | Class "multiGraph" |
| edgeSet-class | Class "multiGraph" |
| edgeSetAM-class | Class "multiGraph" |
| edgeSetIntersect0 | EXPERIMENTAL class "MultiGraph" |
| edgeSetNEL-class | Class "multiGraph" |
| edgeSets | EXPERIMENTAL class "MultiGraph" |
| edgeSets-method | EXPERIMENTAL class "MultiGraph" |
| edgeSetUnion0 | EXPERIMENTAL class "MultiGraph" |
| edgeWeights | Retrieve the edge weights of a graph |
| edgeWeights-method | Class "clusterGraph" |
| edgeWeights-method | Class "distGraph" |
| edgeWeights-method | Class "graph" |
| edgeWeights-method | EXPERIMENTAL class "graphBAM" |
| edgeWeights-method | Class "graphNEL" |
| esetsFemale | MultiGraph edgeSet data |
| esetsMale | MultiGraph edgeSet data |
| eweights | EXPERIMENTAL class "MultiGraph" |
| eWV | Compute an Edge Matrix or weight vector for a Graph |
| extractFromTo | EXPERIMENTAL class "MultiGraph" |
| extractFromTo-method | EXPERIMENTAL class "MultiGraph" |
| extractFromTo-method | EXPERIMENTAL class "graphBAM" |
| extractGraphAM | EXPERIMENTAL class "MultiGraph" |
| extractGraphBAM | EXPERIMENTAL class "MultiGraph" |
-- F --
| fromGXL | Methods for GXL manipulations in package graph |
| fromGXL-method | Methods for GXL manipulations in package graph |
| fromGXL-methods | Methods for GXL manipulations in package graph |
| ftM2adjM | Coercions between matrix and graph representations |
| ftM2graphNEL | Coercions between matrix and graph representations |
| ftM2int | Standard labeling of edges with integers |
-- G --
| graph-class | Class "graph" |
| graph-defunct | Defunct Functions in Package 'graph' |
| graph.par | Graphical parameters and other settings |
| graph.par.get | Graphical parameters and other settings |
| graph2SparseM | Coercion methods between graphs and sparse matrices |
| graphAM | Class "graphAM" |
| graphAM-class | Class "graphAM" |
| graphBAM | EXPERIMENTAL class "graphBAM" |
| graphBAM-class | EXPERIMENTAL class "graphBAM" |
| graphBase-class | Class "graph" |
| graphExamples | A List Of Example Graphs |
| graphIntersect | EXPERIMENTAL class "graphBAM" |
| graphIntersect-method | EXPERIMENTAL class "MultiGraph" |
| graphIntersect-method | EXPERIMENTAL class "graphBAM" |
| graphNEL | Class "graphNEL" |
| graphNEL-class | Class "graphNEL" |
| graphRenderInfo | Class "renderInfo" |
| graphRenderInfo<- | Class "renderInfo" |
| graphUnion | EXPERIMENTAL class "graphBAM" |
| graphUnion-method | EXPERIMENTAL class "MultiGraph" |
| graphUnion-method | EXPERIMENTAL class "graphBAM" |
| GXL | Methods for GXL manipulations in package graph |
| gxlTreeNEL | Methods for GXL manipulations in package graph |
-- I --
| IMCA | KEGG Integrin Mediated Cell Adhesion graph |
| IMCAAttrs | KEGG Integrin Mediated Cell Adhesion graph |
| IMCAGraph | KEGG Integrin Mediated Cell Adhesion graph |
| inEdges | Generic Method inEdges |
| inEdges-method | Class "graphAM" |
| inEdges-method | EXPERIMENTAL class "graphBAM" |
| inEdges-method | Class "graphNEL" |
| initialize | Class "graphNEL" |
| initialize-method | Class "attrData" |
| initialize-method | Class "distGraph" |
| initialize-method | Class "graphAM" |
| initialize-method | EXPERIMENTAL class "graphBAM" |
| initialize-method | Class "graphNEL" |
| int2ftM | Standard labeling of edges with integers |
| integrinMediatedCellAdhesion | KEGG Integrin Mediated Cell Adhesion graph |
| intersection | Class "graph" |
| intersection-method | Class "graph" |
| intersection2 | Class "graph" |
| intersection2-method | Class "graph" |
| isAdjacent | Determine if nodes share an edge in a graph |
| isAdjacent-method | Class "graph" |
| isAdjacent-method | Class "graphAM" |
| isAdjacent-method | EXPERIMENTAL class "graphBAM" |
| isAdjacent-methods | Determine if nodes share an edge in a graph |
| isConnected | Class "graph" |
| isConnected-method | Class "graph" |
| isDirected | Determine if a graph has directed or undirected edges |
| isDirected-method | EXPERIMENTAL class "MultiGraph" |
| isDirected-method | Class "graph" |
| isDirected-method | Class "multiGraph" |
| isDirected-methods | Determine if a graph has directed or undirected edges |
-- J --
| join | Class "graph" |
| join-method | Class "graph" |
-- L --
| leaves | Find the leaves of a graph |
| leaves-method | Find the leaves of a graph |
| listEdges | List the Edges of a Graph |
-- M --
| MAPKsig | A graph encoding parts of the MAPK signaling pathway |
| mgEdgeData | EXPERIMENTAL class "MultiGraph" |
| mgEdgeData-method | EXPERIMENTAL class "MultiGraph" |
| mgEdgeData<- | EXPERIMENTAL class "MultiGraph" |
| mgEdgeData<--method | EXPERIMENTAL class "MultiGraph" |
| mgEdgeDataDefaults | EXPERIMENTAL class "MultiGraph" |
| mgEdgeDataDefaults-method | EXPERIMENTAL class "MultiGraph" |
| mgEdgeDataDefaults<- | EXPERIMENTAL class "MultiGraph" |
| mgEdgeDataDefaults<--method | EXPERIMENTAL class "MultiGraph" |
| mostEdges | Find the node in a graph with the greatest number of edges |
| MultiGraph | EXPERIMENTAL class "MultiGraph" |
| MultiGraph-class | EXPERIMENTAL class "MultiGraph" |
| multiGraph-class | Class "multiGraph" |
-- N --
| names-method | Class "attrData" |
| names<--method | Class "attrData" |
| NELhandler | Methods for GXL manipulations in package graph |
| nodeData | Get and set attributes for the nodes of a graph object |
| nodeData-method | EXPERIMENTAL class "MultiGraph" |
| nodeData-method | Class "graph" |
| nodeData-method | EXPERIMENTAL class "graphBAM" |
| nodeData-methods | Get and set attributes for the nodes of a graph object |
| nodeData<- | Get and set attributes for the nodes of a graph object |
| nodeData<--method | EXPERIMENTAL class "MultiGraph" |
| nodeData<--method | Class "graph" |
| nodeData<--method | EXPERIMENTAL class "graphBAM" |
| nodeData<--methods | Get and set attributes for the nodes of a graph object |
| nodeDataDefaults | Get and set default attributes for the nodes of a graph |
| nodeDataDefaults-method | EXPERIMENTAL class "MultiGraph" |
| nodeDataDefaults-method | Class "graph" |
| nodeDataDefaults-method | EXPERIMENTAL class "graphBAM" |
| nodeDataDefaults-methods | Get and set default attributes for the nodes of a graph |
| nodeDataDefaults<- | Get and set default attributes for the nodes of a graph |
| nodeDataDefaults<--method | EXPERIMENTAL class "MultiGraph" |
| nodeDataDefaults<--method | Class "graph" |
| nodeDataDefaults<--method | EXPERIMENTAL class "graphBAM" |
| nodeDataDefaults<--methods | Get and set default attributes for the nodes of a graph |
| nodeRenderInfo | Class "renderInfo" |
| nodeRenderInfo<- | Class "renderInfo" |
| nodes | Class "graphNEL" |
| nodes-method | EXPERIMENTAL class "MultiGraph" |
| nodes-method | Class "clusterGraph" |
| nodes-method | Class "distGraph" |
| nodes-method | Class "graph" |
| nodes-method | Class "graphAM" |
| nodes-method | EXPERIMENTAL class "graphBAM" |
| nodes-method | Class "graphNEL" |
| nodes-method | Class "multiGraph" |
| nodes<- | Class "graphNEL" |
| nodes<--method | Class "clusterGraph" |
| nodes<--method | Class "graph" |
| nodes<--method | Class "graphAM" |
| nodes<--method | EXPERIMENTAL class "graphBAM" |
| nodes<--method | Class "graphNEL" |
| numEdges | Class "graph" |
| numEdges-method | EXPERIMENTAL class "MultiGraph" |
| numEdges-method | Class "graph" |
| numEdges-method | Class "graphAM" |
| numEdges-method | EXPERIMENTAL class "graphBAM" |
| numEdges-method | Class "multiGraph" |
| numNodes | Class "graph" |
| numNodes-method | EXPERIMENTAL class "MultiGraph" |
| numNodes-method | Class "clusterGraph" |
| numNodes-method | Class "distGraph" |
| numNodes-method | Class "graph" |
| numNodes-method | Class "graphAM" |
| numNodes-method | EXPERIMENTAL class "graphBAM" |
| numNodes-method | Class "graphNEL" |
| numNodes-method | Class "multiGraph" |
| numNoEdges | Calculate the number of nodes that have an edge list of NULL |
-- P --
| pancrCaIni | A graph encoding parts of the pancreatic cancer initiation pathway |
| parRenderInfo | Class "renderInfo" |
| parRenderInfo<- | Class "renderInfo" |
| pathWeights | Compute an Edge Matrix or weight vector for a Graph |
| pkgInstOrder | Defunct Functions in Package 'graph' |
| plot-method | Class "graph" |
-- R --
| randomEGraph | Random Edge Graph |
| randomGraph | Random Graph |
| randomNodeGraph | Generate Random Graph with Specified Degree Distribution |
| removeAttrDataItem<- | Class "attrData" |
| removeAttrDataItem<--method | Class "attrData" |
| removeEdge | removeEdge |
| removeEdge-method | Class "graphAM" |
| removeEdge-method | EXPERIMENTAL class "graphBAM" |
| removeEdge-method | Class "graphNEL" |
| removeEdgesByWeight | EXPERIMENTAL class "graphBAM" |
| removeEdgesByWeight-method | EXPERIMENTAL class "graphBAM" |
| removeNode | removeNode |
| removeNode-method | Class "graphAM" |
| removeNode-method | EXPERIMENTAL class "graphBAM" |
| removeNode-method | Class "graphNEL" |
| renderInfo-class | Class "renderInfo" |
| reverseEdgeDirections | Reverse the edges of a directed graph |
-- S --
| show-method | EXPERIMENTAL class "MultiGraph" |
| show-method | Class "clusterGraph" |
| show-method | Class "distGraph" |
| show-method | Class "graph" |
| show-method | EXPERIMENTAL class "graphBAM" |
| show-method | Class "multiGraph" |
| simpleEdge-class | Class "simpleEdge". |
| sparseM2Graph | Coercion methods between graphs and sparse matrices |
| subGraph | Create a Subgraph |
| subGraph-method | Create a Subgraph |
| subsetEdgeSets | EXPERIMENTAL class "MultiGraph" |
-- T --
| threshold | Class "distGraph" |
| threshold-method | Class "distGraph" |
| toDotR | Methods for Function toDotR, using R to generate a dot serialization |
| toDotR-method | Methods for Function toDotR, using R to generate a dot serialization |
| toDotWithRI | Translate a graph to "dot" including rendering information |
| toGXL | Methods for GXL manipulations in package graph |
| toGXL-method | Class "graphNEL" |
| toGXL-methods | Methods for GXL manipulations in package graph |
-- U --
| ugraph | Underlying Graph |
| ugraph-method | EXPERIMENTAL class "MultiGraph" |
| ugraph-method | EXPERIMENTAL class "graphBAM" |
| ugraph-method | Underlying Graph |
| ugraphOld | Defunct Functions in Package 'graph' |
| union-method | Class "graph" |
| updateGraph | Class "graph" |
| updateGraph-method | Class "graph" |
-- V --
| validateGXL | Methods for GXL manipulations in package graph |
| validateGXL-method | Methods for GXL manipulations in package graph |
| validGraph | Test whether graph object is valid |
-- W --
| write.tlp | Write a graph object in a file in the Tulip format |
-- misc --
| [.dist | Class "distGraph" |