A package that implements some simple graph handling capabilities.

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

Date of publication | None |

Maintainer | Bioconductor Package Maintainer <maintainer@bioconductor.org> |

License | Artistic-2.0 |

Version | 1.52.0 |

**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...

**randomEGraph:** Random Edge Graph

**randomGraph:** Random Graph

**randomNodeGraph:** Generate Random Graph with Specified Degree Distribution

**removeEdge:** removeEdge

**removeNode:** removeNode

**renderInfo-class:** Class "renderInfo"

**reverseEdgeDirections:** Reverse the edges of a directed graph

**settings:** Graphical parameters and other settings

**simpleEdge-class:** Class "simpleEdge".

**standardLabeling:** Standard labeling of edges with integers

**subGraph:** Create a Subgraph

**toDotR-methods:** Methods for Function toDotR, using R to generate a dot...

**toDotWithRI:** Translate a graph to "dot" including rendering information

**ugraph:** Underlying Graph

**validGraph:** Test whether graph object is valid

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

graph/DESCRIPTION

graph/NAMESPACE

graph/R

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

graph/build

graph/build/vignette.rds

graph/data

graph/data/MAPKsig.rda

graph/data/apopGraph.rda

graph/data/biocRepos.rda

graph/data/defunctGraph.rda

graph/data/esetsFemale.rda

graph/data/esetsMale.rda

graph/data/graphExamples.rda

graph/data/integrinMediatedCellAdhesion.rda

graph/data/pancrCaIni.rda

graph/inst

graph/inst/GXL

graph/inst/GXL/attributesExample.gxl

graph/inst/GXL/c2.gxl

graph/inst/GXL/complexExample.gxl

graph/inst/GXL/createGraphExamples.R

graph/inst/GXL/graphExample-01.gxl.gz

graph/inst/GXL/graphExample-02.gxl.gz

graph/inst/GXL/graphExample-03.gxl.gz

graph/inst/GXL/graphExample-04.gxl.gz

graph/inst/GXL/graphExample-05.gxl.gz

graph/inst/GXL/graphExample-06.gxl.gz

graph/inst/GXL/graphExample-07.gxl.gz

graph/inst/GXL/graphExample-08.gxl.gz

graph/inst/GXL/graphExample-09.gxl.gz

graph/inst/GXL/graphExample-10.gxl.gz

graph/inst/GXL/graphExample-11.gxl.gz

graph/inst/GXL/graphExample-12.gxl.gz

graph/inst/GXL/graphExample-13.gxl.gz

graph/inst/GXL/graphExample-14.gxl.gz

graph/inst/GXL/graphExample-15.gxl.gz

graph/inst/GXL/graphExample-16.gxl.gz

graph/inst/GXL/graphExample-17.gxl.gz

graph/inst/GXL/graphExample-18.gxl.gz

graph/inst/GXL/gxl-1.0.1.dtd

graph/inst/GXL/kmstEx.gxl

graph/inst/GXL/outOfOrderExample.gxl

graph/inst/GXL/simplExample.gxl.www

graph/inst/GXL/simpleExample.gxl

graph/inst/Scripts

graph/inst/Scripts/Graph.R

graph/inst/Scripts/distGraph.R

graph/inst/Scripts/multigraph.R

graph/inst/Scripts/pTreetest.R

graph/inst/Scripts/testintersection.R

graph/inst/doc

graph/inst/doc/GraphClass.R

graph/inst/doc/GraphClass.Rnw

graph/inst/doc/GraphClass.pdf

graph/inst/doc/MultiGraphClass.R

graph/inst/doc/MultiGraphClass.Rnw

graph/inst/doc/MultiGraphClass.pdf

graph/inst/doc/clusterGraph.R

graph/inst/doc/clusterGraph.Rnw

graph/inst/doc/clusterGraph.pdf

graph/inst/doc/graph.R

graph/inst/doc/graph.Rnw

graph/inst/doc/graph.pdf

graph/inst/doc/graphAttributes.R

graph/inst/doc/graphAttributes.Rnw

graph/inst/doc/graphAttributes.pdf

graph/inst/perf

graph/inst/perf/Makefile

graph/inst/perf/bgt.R

graph/inst/perf/graphperf.Rnw

graph/inst/perf/multigraphs.Rnw

graph/inst/unitTests

graph/inst/unitTests/MultiGraph_test.R

graph/inst/unitTests/attrData_test.R

graph/inst/unitTests/clusterGraph_test.R

graph/inst/unitTests/degree_test.R

graph/inst/unitTests/edgeWeights_test.R

graph/inst/unitTests/graphAM_test.R

graph/inst/unitTests/graphBAM_test.R

graph/inst/unitTests/graphNEL_test.R

graph/inst/unitTests/gxl_test.R

graph/inst/unitTests/leaves_test.R

graph/inst/unitTests/nodeAndEdgeData_test.R

graph/inst/unitTests/setbit_test.R

graph/inst/unitTests/simple_sparse_test.R

graph/man

graph/man/DFS.Rd
graph/man/IMCA.Rd
graph/man/MAPKsig.Rd
graph/man/MultiGraph-class.Rd
graph/man/acc-methods.Rd
graph/man/addEdge.Rd
graph/man/addNode.Rd
graph/man/adj-methods.Rd
graph/man/adjacencyMatrix.Rd
graph/man/apoptosisGraph.Rd
graph/man/attrData-class.Rd
graph/man/attrDataItem-methods.Rd
graph/man/attrDefaults-methods.Rd
graph/man/aveNumEdges.Rd
graph/man/biocRepos.Rd
graph/man/boundary.Rd
graph/man/calcProb.Rd
graph/man/calcSumProb.Rd
graph/man/clearNode.Rd
graph/man/clusterGraph-class.Rd
graph/man/clusteringCoefficient-methods.Rd
graph/man/combineNodes.Rd
graph/man/defunct.Rd
graph/man/distGraph-class.Rd
graph/man/duplicatedEdges.Rd
graph/man/edgeData-methods.Rd
graph/man/edgeDataDefaults-methods.Rd
graph/man/edgeMatrix.Rd
graph/man/edgeSets.Rd
graph/man/edgeWeights.Rd
graph/man/fromGXL-methods.Rd
graph/man/graph-class.Rd
graph/man/graph2SparseM.Rd
graph/man/graphAM-class.Rd
graph/man/graphBAM-class.Rd
graph/man/graphExamples.Rd
graph/man/graphNEL-class.Rd
graph/man/inEdges.Rd
graph/man/internal.Rd
graph/man/isAdjacent-methods.Rd
graph/man/isDirected-methods.Rd
graph/man/leaves.Rd
graph/man/listEdges.Rd
graph/man/matrix2Graph.Rd
graph/man/mostEdges.Rd
graph/man/multigraph.Rd
graph/man/nodeData-methods.Rd
graph/man/nodeDataDefaults-methods.Rd
graph/man/numNoEdges.Rd
graph/man/pancrCaIni.Rd
graph/man/randomEGraph.Rd
graph/man/randomGraph.Rd
graph/man/randomNodeGraph.Rd
graph/man/removeEdge.Rd
graph/man/removeNode.Rd
graph/man/renderInfo-class.Rd
graph/man/reverseEdgeDirections.Rd
graph/man/settings.Rd
graph/man/simpleEdge-class.Rd
graph/man/standardLabeling.Rd
graph/man/subGraph.Rd
graph/man/toDotR-methods.Rd
graph/man/toDotWithRI.Rd
graph/man/ugraph.Rd
graph/man/validGraph.Rd
graph/man/write.tlp.Rd
graph/src

graph/src/Makevars

graph/src/graph.c

graph/tests

graph/tests/graph_unit_tests.R

graph/vignettes

graph/vignettes/GraphClass.Rnw

graph/vignettes/MultiGraphClass.Rnw

graph/vignettes/clusterGraph.Rnw

graph/vignettes/graph.Rnw

graph/vignettes/graphAttributes.Rnw

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