graph: graph: A package to handle graph data structures

A package that implements some simple graph handling capabilities.

AuthorR. Gentleman, Elizabeth Whalen, W. Huber, S. Falcon
Date of publicationNone
MaintainerBioconductor Package Maintainer <maintainer@bioconductor.org>
LicenseArtistic-2.0
Version1.52.0

View on Bioconductor

Man pages

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

Files in this package

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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