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

Functions

. Man page
acc Man page
acc,clusterGraph,character-method Man page
acc,clusterGraph-method Man page
acc,graph,character-method Man page
acc,graph-method Man page
acc-methods Man page
addEdge Man page
addEdge,character,character,graphAM,missing-method Man page
addEdge,character,character,graphBAM,missing-method Man page
addEdge,character,character,graphBAM,numeric-method Man page
addEdge,character,character,graphNEL,missing-method Man page
addEdge,character,character,graphNEL,numeric-method Man page
addNode Man page
addNode,character,distGraph,list-method Man page
addNode,character,graphAM,missing-method Man page
addNode,character,graphBAM,missing-method Man page
addNode,character,graphNEL,list-method Man page
addNode,character,graphNEL-method Man page
addNode,character,graphNEL,missing-method Man page
adj Man page
adjacencyMatrix Man page
adjacencyMatrix,graphBAM-method Man page
adj,clusterGraph,ANY-method Man page
adj,distGraph,ANY-method Man page
adj,graphBAM,character-method Man page
adj,graphNEL,ANY-method Man page
adj-methods Man page
aM2bpG Man page
apopAttrs Man page
apopGraph Man page
apopLocusLink Man page
attrData-class Man page
attrDataItem Man page
attrDataItem<- Man page
attrDataItem<-,attrData,character,character-method Man page
attrDataItem,attrData,character,character-method Man page
attrDataItem,attrData,character,missing-method Man page
attrDataItem<--methods Man page
attrDataItem-methods Man page
attrDefaults Man page
attrDefaults<- Man page
attrDefaults<-,attrData,character,ANY-method Man page
attrDefaults,attrData,character-method Man page
attrDefaults<-,attrData,missing,list-method Man page
attrDefaults,attrData,missing-method Man page
attrDefaults<--methods Man page
attrDefaults-methods Man page
aveNumEdges Man page
biocRepos Man page
boundary Man page
buildRepDepGraph Man page
calcProb Man page
calcSumProb Man page
clearNode Man page
clearNode,character,graphAM-method Man page
clearNode,character,graphBAM-method Man page
clearNode,character,graphNEL-method Man page
clusterGraph-class Man page
clusterGraph-class Man page
clusteringCoefficient Man page
clusteringCoefficient,graph Man page
clusteringCoefficient,graph-method Man page
coerce Man page
coerce,clusterGraph,matrix-method Man page
coerce,graphAM,graphBAM-method Man page
coerce,graphAM,graphNEL-method Man page
coerce,graphAM,matrix-method Man page
coerce,graphBAM,graphAM-method Man page
coerce,graphBAM,graphNEL-method Man page
coerce,graphBAM,matrix-method Man page
coerce,graphNEL,generalGraph-method Man page
coerce,graphNEL,graphAM-method Man page
coerce,graphNEL,graphBAM-method Man page
coerce,graphNEL,matrix-method Man page
coerce,matrix,graphAM-method Man page
coerce,matrix,graphNEL-method Man page
combineNodes Man page
combineNodes,character,graphNEL,character-method Man page
complement Man page
complement,graph-method Man page
connComp Man page
connComp,clusterGraph-method Man page
connComp,graph-method Man page
degree Man page
degree,graph,ANY-method Man page
degree,graph,missing-method Man page
degree,MultiGraph,missing-method Man page
DFS Man page
DFS,graph,character-method Man page
dfs,graph-method Man page
[.dist Man page
Dist Man page
Dist,distGraph-method Man page
distGraph-class Man page
distGraph-class Man page
dumpGXL Man page
dumpGXL,connection-method Man page
dumpGXL-methods Man page
duplicatedEdges Man page
edgeData Man page
edgeData<- Man page
edgeDataDefaults Man page
edgeDataDefaults<- Man page
edgeDataDefaults<-,graphBAM,character,ANY-method Man page
edgeDataDefaults<-,graphBAM,missing,list-method Man page
edgeDataDefaults<-,graph,character,ANY-method Man page
edgeDataDefaults<-,graph,character-method Man page
edgeDataDefaults,graph,character-method Man page
edgeDataDefaults<-,graph,missing,list-method Man page
edgeDataDefaults,graph,missing-method Man page
edgeDataDefaults<--methods Man page
edgeDataDefaults-methods Man page
edgeData<-,graphBAM,character,character,character,ANY-method Man page
edgeData<-,graphBAM,character,character,character-method Man page
edgeData,graphBAM,character,character,character-method Man page
edgeData<-,graphBAM,character,missing,character,ANY-method Man page
edgeData<-,graphBAM,character,missing,character-method Man page
edgeData,graphBAM,character,missing,character-method Man page
edgeData<-,graphBAM,missing,character,character,ANY-method Man page
edgeData<-,graphBAM,missing,character,character-method Man page
edgeData,graphBAM,missing,character,character-method Man page
edgeData<-,graphBAM,missing,missing,character,ANY-method Man page
edgeData<-,graphBAM,missing,missing,character-method Man page
edgeData,graphBAM,missing,missing,character-method Man page
edgeData,graphBAM,missing,missing,missing-method Man page
edgeData<-,graph,character,character,character,ANY-method Man page
edgeData<-,graph,character,character,character-method Man page
edgeData,graph,character,character,character-method Man page
edgeData,graph,character,character,missing-method Man page
edgeData<-,graph,character,missing,character,ANY-method Man page
edgeData<-,graph,character,missing,character-method Man page
edgeData,graph,character,missing,character-method Man page
edgeData<-,graph,missing,character,character,ANY-method Man page
edgeData<-,graph,missing,character,character-method Man page
edgeData,graph,missing,character,character-method Man page
edgeData,graph,missing,missing,character-method Man page
edgeData,graph,missing,missing,missing-method Man page
edgeData<--methods Man page
edgeData-methods Man page
edgeL Man page
edgeL,clusterGraph-method Man page
edgeL,distGraph-method Man page
edgeL,graph-method Man page
edgeL,graphNEL-method Man page
edgeMatrix Man page
edgeMatrix,clusterGraph-method Man page
edgeMatrix,distGraph-method Man page
edgeMatrix,graphAM-method Man page
edgeMatrix,graphBAM-method Man page
edgeMatrix,graphNEL-method Man page
edgemode Man page
edgemode<- Man page
edgemode,edgeSet-method Man page
edgemode<-,graphBAM,character-method Man page
edgemode<-,graph,character-method Man page
edgemode,graph-method Man page
edgeNames Man page
edgeNames,graph-method Man page
edgeNames,MultiGraph-method Man page
edgeRenderInfo Man page
edgeRenderInfo<- Man page
edges Man page
edges Man page
edges,clusterGraph,character-method Man page
edges,clusterGraph,missing-method Man page
edges,distGraph,character-method Man page
edges,distGraph,missing-method Man page
edges,edgeSetAM,character-method Man page
edges,edgeSetNEL,character-method Man page
edgeSetAM-class Man page
edgeSet-class Man page
edgeSetIntersect0 Man page
edgeSetNEL-class Man page
edgeSets Man page
edgeSets,MultiGraph-method Man page
edgeSetUnion0 Man page
edges,graphAM,character-method Man page
edges,graphAM,missing-method Man page
edges,graphBAM,character-method Man page
edges,graphBAM,missing-method Man page
edges,graphNEL,character-method Man page
edges,graphNEL,missing-method Man page
edges,multiGraph,character-method Man page
edges,MultiGraph,character-method Man page
edges,multiGraph,missing-method Man page
edges,MultiGraph,missing-method Man page
edgeWeights Man page
edgeWeights,clusterGraph,ANY-method Man page
edgeWeights,clusterGraph-method Man page
edgeWeights,distGraph,ANY-method Man page
edgeWeights,distGraph-method Man page
edgeWeights,graphBAM,character-method Man page
edgeWeights,graphBAM-method Man page
edgeWeights,graphBAM,missing-method Man page
edgeWeights,graphBAM,numeric-method Man page
edgeWeights,graph,character-method Man page
edgeWeights,graph,missing-method Man page
edgeWeights,graphNEL-method Man page
edgeWeights,graph,numeric-method Man page
esetsFemale Man page
esetsMale Man page
eweights Man page
eWV Man page
extractFromTo Man page
extractFromTo,graphBAM-method Man page
extractFromTo,MultiGraph-method Man page
extractGraphAM Man page
extractGraphBAM Man page
fromGXL Man page
fromGXL,connection-method Man page
fromGXL-methods Man page
ftM2adjM Man page
ftM2graphNEL Man page
ftM2int Man page
graph2SparseM Man page
graphAM Man page
graphAM-class Man page
graphBAM Man page
graphBAM-class Man page
graphBase-class Man page
graph-class Man page
graph-defunct Man page
graphExamples Man page
graphIntersect Man page
graphIntersect,graphBAM,graphBAM-method Man page
graphIntersect,MultiGraph,MultiGraph-method Man page
graphNEL Man page
graphNEL-class Man page
graph.par Man page
graph.par.get Man page
graphRenderInfo Man page
graphRenderInfo<- Man page
graphUnion Man page
graphUnion,graphBAM,graphBAM-method Man page
graphUnion,MultiGraph,MultiGraph-method Man page
GXL Man page
gxlTreeNEL Man page
IMCA Man page
IMCAAttrs Man page
IMCAGraph Man page
inEdges Man page
inEdges,character,graphAM-method Man page
inEdges,character,graphBAM-method Man page
inEdges,character,graphNEL-method Man page
inEdges,graphAM,missing-method Man page
inEdges,graphNEL,missing-method Man page
inEdges,missing,graphAM-method Man page
inEdges,missing,graphNEL-method Man page
initialize Man page
initialize,attrData-method Man page
initialize,distGraph-method Man page
initialize,graphAM-method Man page
initialize,graphBAM-method Man page
initialize,graphNEL-method Man page
int2ftM Man page
integrinMediatedCellAdhesion Man page
intersection Man page
intersection2 Man page
intersection2,graph,graph-method Man page
intersection,graph,graph-method Man page
isAdjacent Man page
isAdjacent,graphAM,character,character-method Man page
isAdjacent,graphBAM,character,character-method Man page
isAdjacent,graph,character,character-method Man page
isAdjacent-methods Man page
isConnected Man page
isConnected,graph-method Man page
isDirected Man page
isDirected,DiEdgeSet-method Man page
isDirected,edgeSet-method Man page
isDirected,graph-method Man page
isDirected-methods Man page
isDirected,multiGraph-method Man page
isDirected,MultiGraph-method Man page
isDirected,UEdgeSet-method Man page
join Man page
join,graph,graph-method Man page
leaves Man page
leaves,graph-method Man page
listEdges Man page
MAPKsig Man page
mgEdgeData Man page
mgEdgeData<- Man page
mgEdgeDataDefaults Man page
mgEdgeDataDefaults<- Man page
mgEdgeDataDefaults<-,MultiGraph,character,character,ANY-method Man page
mgEdgeDataDefaults,MultiGraph,character,character-method Man page
mgEdgeDataDefaults<-,MultiGraph,character,missing,list-method Man page
mgEdgeDataDefaults,MultiGraph,character,missing-method Man page
mgEdgeData<-,MultiGraph,character,character,character,character- Man page
mgEdgeData,MultiGraph,character,character,character,character-me Man page
mgEdgeData<-,MultiGraph,character,character,missing,character-me Man page
mgEdgeData,MultiGraph,character,character,missing,character-meth Man page
mgEdgeData<-,MultiGraph,character,missing,character,character-me Man page
mgEdgeData,MultiGraph,character,missing,character,character-meth Man page
mgEdgeData<-,MultiGraph,character,missing,missing,character-meth Man page
mgEdgeData,MultiGraph,character,missing,missing,character-method Man page
mostEdges Man page
MultiGraph Man page
multiGraph-class Man page
MultiGraph-class Man page
names<-,attrData,character-method Man page
names,attrData-method Man page
NELhandler Man page
nodeData Man page
nodeData<- Man page
nodeDataDefaults Man page
nodeDataDefaults<- Man page
nodeDataDefaults<-,graphBAM,character,ANY-method Man page
nodeDataDefaults,graphBAM,character-method Man page
nodeDataDefaults<-,graphBAM,missing,ANY-method Man page
nodeDataDefaults<-,graphBAM,missing,list-method Man page
nodeDataDefaults,graphBAM,missing-method Man page
nodeDataDefaults<-,graph,character,ANY-method Man page
nodeDataDefaults<-,graph,character-method Man page
nodeDataDefaults,graph,character-method Man page
nodeDataDefaults<-,graph,missing,list-method Man page
nodeDataDefaults,graph,missing-method Man page
nodeDataDefaults<--methods Man page
nodeDataDefaults-methods Man page
nodeDataDefaults<-,MultiGraph,character,ANY-method Man page
nodeDataDefaults,MultiGraph,character-method Man page
nodeDataDefaults<-,MultiGraph,missing,list-method Man page
nodeDataDefaults,MultiGraph,missing-method Man page
nodeData<-,graphBAM,character,character-method Man page
nodeData,graphBAM,character,character-method Man page
nodeData,graphBAM,character,missing-method Man page
nodeData<-,graphBAM,missing,character-method Man page
nodeData,graphBAM,missing,character-method Man page
nodeData,graphBAM,missing,missing-method Man page
nodeData<-,graph,character,character-method Man page
nodeData,graph,character,character-method Man page
nodeData,graph,character,missing-method Man page
nodeData<-,graph,missing,character-method Man page
nodeData,graph,missing,character-method Man page
nodeData,graph,missing,missing-method Man page
nodeData<--methods Man page
nodeData-methods Man page
nodeData<-,MultiGraph,character,character-method Man page
nodeData,MultiGraph,character,character-method Man page
nodeData,MultiGraph,character,missing-method Man page
nodeData<-,MultiGraph,missing,character-method Man page
nodeData,MultiGraph,missing,character-method Man page
nodeData,MultiGraph,missing,missing-method Man page
nodeRenderInfo Man page
nodeRenderInfo<- Man page
nodes Man page
nodes<- Man page
nodes<-,clusterGraph,character-method Man page
nodes,clusterGraph-method Man page
nodes,distGraph-method Man page
nodes,edgeSetAM-method Man page
nodes<-,graphAM,character-method Man page
nodes,graphAM-method Man page
nodes<-,graphBAM,character-method Man page
nodes,graphBAM-method Man page
nodes<-,graph,character-method Man page
nodes,graph-method Man page
nodes<-,graphNEL,character-method Man page
nodes,graphNEL-method Man page
nodes,multiGraph-method Man page
nodes,MultiGraph-method Man page
nullgraphID Man page
numEdges Man page
numEdges,edgeSetAM-method Man page
numEdges,graphAM-method Man page
numEdges,graphBAM-method Man page
numEdges,graph-method Man page
numEdges,MGEdgeSet-method Man page
numEdges,multiGraph-method Man page
numEdges,MultiGraph-method Man page
numNodes Man page
numNodes,clusterGraph-method Man page
numNodes,distGraph-method Man page
numNodes,graphAM-method Man page
numNodes,graphBAM-method Man page
numNodes,graph-method Man page
numNodes,graphNEL-method Man page
numNodes,multiGraph-method Man page
numNodes,MultiGraph-method Man page
numNoEdges Man page
pancrCaIni Man page
parRenderInfo Man page
parRenderInfo<- Man page
pathWeights Man page
pkgInstOrder Man page
plot,graph,ANY-method Man page
randomEGraph Man page
randomGraph Man page
randomNodeGraph Man page
removeAttrDataItem<- Man page
removeAttrDataItem<-,attrData,character,NULL-method Man page
removeEdge Man page
removeEdge,character,character,graphAM-method Man page
removeEdge,character,character,graphBAM-method Man page
removeEdge,character,character,graphNEL-method Man page
removeEdgesByWeight Man page
removeEdgesByWeight,graphBAM-method Man page
removeNode Man page
removeNode,character,graphAM-method Man page
removeNode,character,graphBAM-method Man page
removeNode,character,graphNEL-method Man page
renderInfo-class Man page
reverseEdgeDirections Man page
show,clusterGraph-method Man page
show,distGraph-method Man page
show,edgeSet-method Man page
show,graphBAM-method Man page
show,graph-method Man page
show,multiGraph-method Man page
show,MultiGraph-method Man page
simpleEdge-class Man page
sparseM2Graph Man page
subGraph Man page
subGraph,character,clusterGraph-method Man page
subGraph,character,distGraph-method Man page
subGraph,character,graphBAM-method Man page
subGraph,character,graphNEL-method Man page
subGraph,character,MultiGraph-method Man page
subsetEdgeSets Man page
threshold Man page
threshold,distGraph-method Man page
toDotR Man page
toDotR,graphNEL,character,list,list-method Man page
toDotR,graphNEL,character,missing,list-method Man page
toDotR,graphNEL,character,missing,missing-method Man page
toDotR,graphNEL,missing,character,missing-method Man page
toDotR,graphNEL,missing,list,list-method Man page
toDotR,graphNEL,missing,list,missing-method Man page
toDotR,graphNEL,missing,missing,list-method Man page
toDotR,graphNEL,missing,missing,missing-method Man page
toDotWithRI Man page
toGXL Man page
toGXL,graphNEL-method Man page
toGXL-methods Man page
ugraph Man page
ugraph,DiEdgeSet-method Man page
ugraph,graphBAM-method Man page
ugraph,graph-method Man page
ugraph,MultiGraph-method Man page
ugraphOld Man page
ugraph,UEdgeSet-method Man page
union,graph,graph-method Man page
updateGraph Man page
updateGraph,graph-method Man page
validateGXL Man page
validateGXL,connection-method Man page
validGraph Man page
write.tlp Man page

Files

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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