graph: A package to handle graph data structures

Vignettes

- Attributes for Graph Objects
- clusterGraph and distGraph
- Graph
- graphBAM and MultiGraph classes
- Graph Design

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**acc-methods:**Methods for Accessibility Lists**addEdge:**addEdge**addNode:**addNode**adjacencyMatrix:**Compute an Adjacency Matrix for a graphBAM object**adj-methods:**Methods for finding the adjacency list for selected nodes.**apoptosisGraph:**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**calcProb:**Calculate the hypergeometric probability of the subgraph's...**calcSumProb:**Calculate the probability that a subgraph has an unusual...**clearNode:**clearNode**clusterGraph-class:**Class "clusterGraph"**clusteringCoefficient-methods:**Clustering coefficient of a graph**combineNodes:**combineNodes**defunct:**Defunct Functions in Package 'graph'**DFS:**Depth First Search**distGraph-class:**Class "distGraph"**duplicatedEdges:**duplicatedEdges**edgeDataDefaults-methods:**Get and set default attributes for the edges of a graph**edgeData-methods:**Get and set attributes for the edges of a graph object**edgeMatrix:**Compute an Edge Matrix or weight vector for a Graph**edgeSets:**MultiGraph edgeSet data**edgeWeights:**Retrieve the edge weights of a graph**fromGXL-methods:**Methods for GXL manipulations in package graph**graph2SparseM:**Coercion methods between graphs and sparse matrices**graphAM-class:**Class "graphAM"**graphBAM-class:**EXPERIMENTAL class "graphBAM"**graph-class:**Class "graph"**graphExamples:**A List Of Example Graphs**graphNEL-class:**Class "graphNEL"**IMCA:**KEGG Integrin Mediated Cell Adhesion graph**inEdges:**Generic Method inEdges**internal:**Variables used for internal purposes**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**MAPKsig:**A graph encoding parts of the MAPK signaling pathway**matrix2Graph:**Coercions between matrix and graph representations**mostEdges:**Find the node in a graph with the greatest number of edges**multigraph:**Class "multiGraph"**MultiGraph-class:**EXPERIMENTAL class "MultiGraph"**nodeDataDefaults-methods:**Get and set default attributes for the nodes of a graph**nodeData-methods:**Get and set attributes for the nodes of a graph object**numNoEdges:**Calculate the number of nodes that have an edge list of NULL**pancrCaIni:**A graph encoding parts of the pancreatic cancer initiation...**Browse all...**

The `nullgraphID`

variable is used to store a default
identifier. This should not be used by users.

Saikat DebRoy

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