graph: graph: A package to handle graph data structures

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

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