# graph v1.50.0

## graph: A package to handle graph data structures

A package that implements some simple graph handling
capabilities.

## Functions in graph

Name | Description | |

acc-methods | Methods for Accessibility Lists | |

removeNode | removeNode | |

removeEdge | removeEdge | |

mostEdges | Find the node in a graph with the greatest number of edges | |

pancrCaIni | A graph encoding parts of the pancreatic cancer initiation pathway | |

pathwayGraph | Graph representing the topology of a pathway | |

Pathways-class | Class "Pathways" | |

leaves | Find the leaves of a graph | |

integrinMediatedCellAdhesion | KEGG Integrin Mediated Cell Adhesion graph | |

calcSumProb | Calculate the probability that a subgraph has an unusual number of edges. | |

attrData-class | Class "attrData" | |

toDotR-methods | Methods for Function toDotR, using R to generate a dot serialization | |

DFS | Depth First Search | |

kegg | KEGG pathways | |

runSPIA | Run SPIA analysis | |

boundary | Returns the Boundary between a Graph and a SubGraph | |

nodeDataDefaults-methods | Get and set default attributes for the nodes of a graph | |

distGraph-class | Class "distGraph" | |

MAPKsig | A graph encoding parts of the MAPK signaling pathway | |

biocRepos | A graph representing the Bioconductor package repository | |

ugraph | Underlying Graph | |

graph2SparseM | Coercion methods between graphs and sparse matrices | |

addNode | addNode | |

apoptosisGraph | KEGG apoptosis pathway graph | |

Pathway-class | Class "Pathway" | |

multiGraph-class | Class "multiGraph" | |

pathways | Retrieve a list of pathways. | |

inEdges | Generic Method inEdges | |

reactome | Reactome pathways | |

as.list.PathwayList | Convertion of PathwayLists into lists. | |

runTopologyGSA | Run a topological analysis on an expression dataset using topologyGSA. | |

biocarta | BioCarta pathways | |

humancyc | Humancyc pathways | |

prepareSPIA | Prepare pathway dataset needed by runSPIA. | |

validGraph | Test whether graph object is valid | |

buildPathway | Build a Pathway object. | |

isDirected-methods | Determine if a graph has directed or undirected edges | |

toDotWithRI | Translate a graph to "dot" including rendering information | |

pathwayDatabases | List the available pathway databases. | |

combineNodes | combineNodes | |

attrDataItem-methods | Get and set attributes values for items in an attrData object | |

edgeMatrix | Compute an Edge Matrix or weight vector for a Graph | |

edgeSets | MultiGraph edgeSet data | |

attrDefaults-methods | Get and set the default attributes of an attrData object | |

graphExamples | A List Of Example Graphs | |

addEdge | addEdge | |

numNoEdges | Calculate the number of nodes that have an edge list of NULL | |

isAdjacent-methods | Determine if nodes share an edge in a graph | |

nci | NCI pathways | |

reverseEdgeDirections | Reverse the edges of a directed graph | |

panther | Panther pathways | |

convertIdentifiers | Convert the node identifiers of a pathway. | |

aveNumEdges | Calculate the average number of edges in a graph | |

adjacencyMatrix | Compute an Adjacency Matrix for a graphBAM object | |

calcProb | Calculate the hypergeometric probability of the subgraph's number of edges. | |

clearNode | clearNode | |

graphAM-class | Class "graphAM" | |

graphNEL-class | Class "graphNEL" | |

write.tlp | Write a graph object in a file in the Tulip format | |

DeprecatedPathwayList-class | Class "DeprecatedPathwayList" | |

Standard labeling of edges with integers | Standard labeling of edges with integers | |

renderInfo-class | Class "renderInfo" | |

clusterGraph-class | Class "clusterGraph" | |

graph-defunct | Defunct Functions in Package graph | |

duplicatedEdges | duplicatedEdges | |

edgeData-methods | Get and set attributes for the edges of a graph object | |

edgeWeights | Retrieve the edge weights of a graph | |

as.list.DeprecatedPathwayList | Convertion of DeprecatedPathwayLists into lists. | |

Coercions between matrix and graph representations | Coercions between matrix and graph representations | |

cytoscapePlot | Plot a pathway graph in Cytoscape | |

simpleEdge-class | Class "simpleEdge". | |

runDEGraph | Run a topological analysis on an expression dataset using DEGraph package. | |

runClipper | Run a topological analysis on an expression dataset using clipper. | |

runTopologyGSAMulti | Run a topological analysis on an expression dataset using topologyGSA. | |

runDEGraphMulti | Run a topological analysis on an expression dataset using DEGraph package. | |

adj-methods | Methods for finding the adjacency list for selected nodes. | |

fromGXL-methods | Methods for GXL manipulations in package graph | |

graph-class | Class "graph" | |

edgeDataDefaults-methods | Get and set default attributes for the edges of a graph | |

randomEGraph | Random Edge Graph | |

PathwayList-class | Class "PathwayList" | |

randomNodeGraph | Generate Random Graph with Specified Degree Distribution | |

runClipperMulti | Run a topological analysis on an expression dataset using clipper. | |

clusteringCoefficient-methods | Clustering coefficient of a graph | |

graphBAM-class | EXPERIMENTAL class "graphBAM" | |

listEdges | List the Edges of a Graph | |

nodeData-methods | Get and set attributes for the nodes of a graph object | |

randomGraph | Random Graph | |

graph.par | Graphical parameters and other settings | |

internal | Variables used for internal purposes | |

subGraph | Create a Subgraph | |

No Results! |

## Last year downloads

## Details

License | Artistic-2.0 |

Collate | AllClasses.R AllGenerics.R bitarray.R buildDepGraph.R methods-graph.R graphNEL.R clustergraph.R NELhandler.R edgefunctions.R graphfunctions.R GXLformals.R gxlReader.R random.R write.tlp.R mat2graph.R settings.R zzz.R standardLabeling.R TODOT.R toDotWithRI.R methods-graphAM.R attrData.R reverseEdgeDirections.R nodes-methods.R methods-multiGraph.R test_graph_package.R MultiGraph.R methods-graphBAM.R graph-constructors.R |

LazyLoad | yes |

Packaged | 2012-04-28 03:51:46 UTC; biocbuild |

biocViews | GraphAndNetwork |

depends | base (>= 2.10) , BiocGenerics (>= 0.13.11) , methods , R (>= 2.10) |

suggests | cluster , RBGL , RUnit , SparseM (>= 0.36) , XML |

enhances | Rgraphviz |

imports | stats , stats4 , utils |

Contributors | R. Gentleman, W. Huber, Elizabeth Whalen, S. Falcon |

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