graph: graph: A package to handle graph data structures
Version 1.54.0

A package that implements some simple graph handling capabilities.

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AuthorR. Gentleman, Elizabeth Whalen, W. Huber, S. Falcon
Bioconductor views GraphAndNetwork
Date of publicationNone
MaintainerBioconductor Package Maintainer <maintainer@bioconductor.org>
LicenseArtistic-2.0
Version1.54.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("graph")

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
DFS Man page
DFS,graph,character-method Man page
Dist Man page
Dist,distGraph-method Man page
GXL Man page
IMCA Man page
IMCAAttrs Man page
IMCAGraph Man page
MAPKsig Man page
MultiDiGraph Source code
MultiGraph Man page Source code
MultiGraph-class Man page
NEL2mat Source code
NELhandler Man page Source code
[.dist Man page
aM2bpG Man page Source code
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
addDefaultAttrs Source code
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,missing-method Man page
addNode,character,graphNEL-method Man page
adj 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
adjacencyMatrix Man page
adjacencyMatrix,graphBAM-method Man page
align_from_to Source code
apopAttrs Man page
apopGraph Man page
apopLocusLink Man page
attrData-class Man page
attrDataItem Man page
attrDataItem,attrData,character,character-method Man page
attrDataItem,attrData,character,missing-method Man page
attrDataItem-methods Man page
attrDataItem<- Man page
attrDataItem<-,attrData,character,character-method Man page
attrDataItem<--methods Man page
attrDefaults Man page
attrDefaults,attrData,character-method Man page
attrDefaults,attrData,missing-method Man page
attrDefaults-methods Man page
attrDefaults<- Man page
attrDefaults<-,attrData,character,ANY-method Man page
attrDefaults<-,attrData,missing,list-method Man page
attrDefaults<--methods Man page
aveNumEdges Man page Source code
bamIntersect Source code
bamUnion Source code
biocRepos Man page
bitToInteger Source code
bitToLogical Source code
bitToMat Source code
bitdim Source code
bitlen Source code
boundary Man page Source code
buildRepDepGraph Man page Source code
calcProb Man page Source code
calcSumProb Man page Source code
checkAttrLength Source code
checkValidNodeName Source code
clearEdgeData Source code
clearNode Man page
clearNode,character,graphAM-method Man page
clearNode,character,graphBAM-method Man page
clearNode,character,graphNEL-method Man page
clearNodeData Source code
clusterGraph-class Man page 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
columnIndex Source code
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
coordToIndex Source code Source code
createZeroBitPos Source code
default.graph.pars Source code
degree Man page
degree,MultiGraph,missing-method Man page
degree,graph,ANY-method Man page
degree,graph,missing-method Man page
dfs,graph-method Man page
diEdgeSetToDataFrame Source code
distGraph-class Man page Man page
dropEdges Source code
dumpGXL Man page
dumpGXL,connection-method Man page
dumpGXL-methods Man page
duplicatedEdges Man page Source code
eAttrsFun Source code
eWV Man page Source code
edgeData Man page
edgeData,graph,character,character,character-method Man page
edgeData,graph,character,character,missing-method Man page
edgeData,graph,character,missing,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,graphBAM,character,character,character-method Man page
edgeData,graphBAM,character,missing,character-method Man page
edgeData,graphBAM,missing,character,character-method Man page
edgeData,graphBAM,missing,missing,character-method Man page
edgeData,graphBAM,missing,missing,missing-method Man page
edgeData-methods Man page
edgeData<- Man page
edgeData<-,graph,character,character,character,ANY-method Man page
edgeData<-,graph,character,character,character-method Man page
edgeData<-,graph,character,missing,character,ANY-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<-,graphBAM,character,character,character,ANY-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,missing,character,character,ANY-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<--methods Man page
edgeDataDefaults Man page
edgeDataDefaults,graph,character-method Man page
edgeDataDefaults,graph,missing-method Man page
edgeDataDefaults-methods Man page
edgeDataDefaults<- Man page
edgeDataDefaults<-,graph,character,ANY-method Man page
edgeDataDefaults<-,graph,character-method Man page
edgeDataDefaults<-,graph,missing,list-method Man page
edgeDataDefaults<-,graphBAM,character,ANY-method Man page
edgeDataDefaults<-,graphBAM,missing,list-method Man page
edgeDataDefaults<--methods Man page
edgeKiller Source code
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
edgeNames Man page
edgeNames,MultiGraph-method Man page
edgeNames,graph-method Man page
edgeRenderInfo Man page Source code
edgeRenderInfo<- Man page
edgeSet-class Man page
edgeSetAM-class Man page
edgeSetIntersect0 Man page Source code
edgeSetNEL-class Man page
edgeSetToMatrix Source code
edgeSetUnion0 Man page Source code
edgeSets Man page
edgeSets,MultiGraph-method Man page
edgeWeight Source code
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,graph,character-method Man page
edgeWeights,graph,missing-method Man page
edgeWeights,graph,numeric-method Man page
edgeWeights,graphBAM,character-method Man page
edgeWeights,graphBAM,missing-method Man page
edgeWeights,graphBAM,numeric-method Man page
edgeWeights,graphBAM-method Man page
edgeWeights,graphNEL-method Man page
edgemode Man page
edgemode,edgeSet-method Man page
edgemode,graph-method Man page
edgemode<- Man page
edgemode<-,graph,character-method Man page
edgemode<-,graphBAM,character-method Man page
edges Man page Man page
edges,MultiGraph,character-method Man page
edges,MultiGraph,missing-method 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
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,missing-method Man page
edges_gbam Source code
edges_mg Source code
esetsFemale Man page
esetsMale Man page
eweights Man page Source code
extendAdjMat Source code
extractFromTo Man page
extractFromTo,MultiGraph-method Man page
extractFromTo,graphBAM-method Man page
extractFromTo_mg Source code
extractGraphAM Man page Source code
extractGraphBAM Man page Source code
fromGXL Man page
fromGXL,connection-method Man page
fromGXL-methods Man page
ftM2adjM Man page Source code
ftM2graphNEL Man page Source code
ftM2int Man page Source code
ftM2other Source code
getAllEdges Source code
getBAMIntersect Source code
getBitCell Source code
getColumn Source code
getEdgeIntersect Source code
getEdgeKeys Source code
getEdgeList Source code
getIndices Source code
getIntNodeUserAttrPos Source code
getIntersectAttrs Source code
getIntersectEdgeUserAttrPos Source code
getMGIntersect Source code
getMGUnionAttrs Source code
getMGUnionWeights Source code
getNodeAttrOrder Source code
getNodeAttrPos Source code
getNodeAttrVec Source code
getNodeIndex Source code
getObjectSlots Source code
getRow Source code
getUnionAttrs Source code
getUnionEdgeSet Source code
getUnionNodeUserAttrPos Source code
getUnionWeights Source code
getWeightList2 Source code
get_edgeData_indicies Source code
graph-class Man page
graph-defunct Man page
graph.par Man page Source code
graph.par.get Man page Source code
graph2SparseM Man page Source code
graphAM Man page Source code
graphAM-class Man page
graphBAM Man page Source code
graphBAM-class Man page
graphBase-class Man page
graphExamples Man page
graphIntersect Man page
graphIntersect,MultiGraph,MultiGraph-method Man page
graphIntersect,graphBAM,graphBAM-method Man page
graphNEL Man page Source code
graphNEL-class Man page
graphNEL_init_edgeL_weights Source code
graphNEL_init_edges Source code
graphNEL_init_edges_nested Source code
graphNELhandler Source code
graphRenderInfo Man page Source code
graphRenderInfo<- Man page
graphToBAM Source code
graphUnion Man page
graphUnion,MultiGraph,MultiGraph-method Man page
graphUnion,graphBAM,graphBAM-method Man page
graph_handler Source code
gxlTreeNEL Man page Source code
hasEdgemode Source code
inE Source code
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
inOutCounts Source code
initEdgeSet Source code
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 Source code
integrinMediatedCellAdhesion Man page
intersection Man page
intersection,graph,graph-method Man page
intersection2 Man page
intersection2,graph,graph-method Man page
isAdjacent Man page
isAdjacent,graph,character,character-method Man page
isAdjacent,graphAM,character,character-method Man page
isAdjacent,graphBAM,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,MultiGraph-method Man page
isDirected,UEdgeSet-method Man page
isDirected,edgeSet-method Man page
isDirected,graph-method Man page
isDirected,multiGraph-method Man page
isDirected-methods Man page
isUpToDate Source code
isValidAdjMat Source code
isValidNodeList Source code
join Man page
join,graph,graph-method Man page
leaves Man page
leaves,graph-method Man page
listEdges Man page Source code
listLen Source code
makeEdgeKeys Source code
makeMDEdgeSet Source code
makeMDEdgeSets Source code
makebits Source code
mgDegree Source code
mgEdgeData Man page
mgEdgeData,MultiGraph,character,character,character,character-me Man page
mgEdgeData,MultiGraph,character,character,missing,character-meth Man page
mgEdgeData,MultiGraph,character,missing,character,character-meth Man page
mgEdgeData,MultiGraph,character,missing,missing,character-method Man page
mgEdgeData<- Man page
mgEdgeData<-,MultiGraph,character,character,character,character- Man page
mgEdgeData<-,MultiGraph,character,character,missing,character-me Man page
mgEdgeData<-,MultiGraph,character,missing,character,character-me Man page
mgEdgeData<-,MultiGraph,character,missing,missing,character-meth Man page
mgEdgeDataDefaults Man page
mgEdgeDataDefaults,MultiGraph,character,character-method Man page
mgEdgeDataDefaults,MultiGraph,character,missing-method Man page
mgEdgeDataDefaults<- Man page
mgEdgeDataDefaults<-,MultiGraph,character,character,ANY-method Man page
mgEdgeDataDefaults<-,MultiGraph,character,missing,list-method Man page
mgGetAttrs Source code
mgIsAdj Source code
mgSetAttrs Source code
mg_node_names Source code
mg_undirectEdges Source code
mg_valid_node_names Source code
mg_validate_edgeSet Source code
mg_validate_node_names Source code
mostEdges Man page Source code
multiGraph-class Man page
names,attrData-method Man page
names<-,attrData,character-method Man page
nbitset Source code
ndexToCoord Source code
nodeData 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,missing-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,missing-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,missing-method Man page
nodeData-methods Man page
nodeData<- Man page
nodeData<-,MultiGraph,character,character-method Man page
nodeData<-,MultiGraph,missing,character-method Man page
nodeData<-,graph,character,character-method Man page
nodeData<-,graph,missing,character-method Man page
nodeData<-,graphBAM,character,character-method Man page
nodeData<-,graphBAM,missing,character-method Man page
nodeData<--methods Man page
nodeDataDefaults Man page
nodeDataDefaults,MultiGraph,character-method Man page
nodeDataDefaults,MultiGraph,missing-method Man page
nodeDataDefaults,graph,character-method Man page
nodeDataDefaults,graph,missing-method Man page
nodeDataDefaults,graphBAM,character-method Man page
nodeDataDefaults,graphBAM,missing-method Man page
nodeDataDefaults-methods Man page
nodeDataDefaults<- Man page
nodeDataDefaults<-,MultiGraph,character,ANY-method Man page
nodeDataDefaults<-,MultiGraph,missing,list-method Man page
nodeDataDefaults<-,graph,character,ANY-method Man page
nodeDataDefaults<-,graph,character-method Man page
nodeDataDefaults<-,graph,missing,list-method Man page
nodeDataDefaults<-,graphBAM,character,ANY-method Man page
nodeDataDefaults<-,graphBAM,missing,ANY-method Man page
nodeDataDefaults<-,graphBAM,missing,list-method Man page
nodeDataDefaults<--methods Man page
nodeDataReplaceNodeGiven Source code
nodeDataReplaceNodeMissing Source code
nodeDataRetrieve Source code
nodeIntersect Source code
nodeRenderInfo Man page Source code
nodeRenderInfo<- Man page
nodeUnion Source code
node_rename_check Source code
nodes Man page
nodes,MultiGraph-method Man page
nodes,clusterGraph-method Man page
nodes,distGraph-method Man page
nodes,edgeSetAM-method Man page
nodes,graph-method Man page
nodes,graphAM-method Man page
nodes,graphBAM-method Man page
nodes,graphNEL-method Man page
nodes,multiGraph-method Man page
nodes<- Man page
nodes<-,clusterGraph,character-method Man page
nodes<-,graph,character-method Man page
nodes<-,graphAM,character-method Man page
nodes<-,graphBAM,character-method Man page
nodes<-,graphNEL,character-method Man page
normalizeEdges Source code
nullgraphID Man page
numEdges Man page
numEdges,MGEdgeSet-method Man page
numEdges,MultiGraph-method Man page
numEdges,edgeSetAM-method Man page
numEdges,graph-method Man page
numEdges,graphAM-method Man page
numEdges,graphBAM-method Man page
numEdges,multiGraph-method Man page
numNoEdges Man page Source code
numNodes Man page
numNodes,MultiGraph-method Man page
numNodes,clusterGraph-method Man page
numNodes,distGraph-method Man page
numNodes,graph-method Man page
numNodes,graphAM-method Man page
numNodes,graphBAM-method Man page
numNodes,graphNEL-method Man page
numNodes,multiGraph-method Man page
nvertListOfLists Source code
onUnload Source code
oneWeights Source code
pancrCaIni Man page
parRenderInfo Man page Source code
parRenderInfo<- Man page
pasteq Source code
pathWeights Man page Source code
pkgInstOrder Man page Source code
plot,graph,ANY-method Man page
print_attr_list Source code
print_attr_stmt Source code
print_edge_stmt Source code
print_node_stmt Source code
print_stmt_list_fromGraph Source code
print_subgraph Source code
qrequire Source code
randFromTo Source code
randomEGraph Man page Source code
randomGraph Man page Source code
randomNodeGraph Man page Source code
remEdge Source code
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
rename_edge_attributes Source code
rename_node_attributes Source code
renderInfo-class Man page
report_duplicate_edges Source code
retAttrVec Source code
retEdgeIntersectDefaults Source code
retEdgeUnionDefaults Source code
retMGAttrVec Source code
retMGEdgeUnionDefaults Source code
retMGEdgeUnionUserAttrPos Source code
retNodeIntersectDefaults Source code
retNodeUnionDefaults Source code
reverseEdgeDirections Man page Source code
rowIndex Source code
scaleEdgeSet Source code
scaleGraphBAM Source code
scaleMG Source code
scaleUserAttrPos Source code
setBitCell Source code
setRenderInfo Source code
set_attrs Source code
setbit Source code
setbitv Source code
show,MultiGraph-method Man page
show,clusterGraph-method Man page
show,distGraph-method Man page
show,edgeSet-method Man page
show,graph-method Man page
show,graphBAM-method Man page
show,multiGraph-method Man page
simpleEdge-class Man page
sparseM2Graph Man page Source code
splitEdgeRenderInfo Source code
splitNodeRenderInfo Source code
splitRenderInfo Source code
subGraph Man page
subGraph,character,MultiGraph-method 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
subsetEdgeSets Man page Source code
sumbits Source code
swapNames Source code
test Source code
testbit Source code
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 Source code
toGXL Man page
toGXL,graphNEL-method Man page
toGXL-methods Man page
ugraph Man page
ugraph,DiEdgeSet-method Man page
ugraph,MultiGraph-method Man page
ugraph,UEdgeSet-method Man page
ugraph,graph-method Man page
ugraph,graphBAM-method Man page
ugraphOld Man page Source code
undirectEdges Source code
union,graph,graph-method Man page
updateFolder Source code
updateGraph Man page
updateGraph,graph-method Man page
validGraph Man page Source code
validateGXL Man page
validateGXL,connection-method Man page
verifyAttrListNames Source code
verifyAttrName Source code
verifyBAMAttrs Source code
verifyEdges Source code
verifyMGAttrs Source code
verifyMgEdgeSetNames Source code
verifyMgEdges Source code
verifyNodes Source code
wrapAttrVal Source code
wrapID Source code
write.tlp Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.R
R/AllGenerics.R
R/GXLformals.R
R/MultiGraph.R
R/NELhandler.R
R/TODOT.R
R/attrData.R
R/bitarray.R
R/buildDepGraph.R
R/clustergraph.R
R/edgefunctions.R
R/graph-constructors.R
R/graphNEL.R
R/graphfunctions.R
R/gxlReader.R
R/mat2graph.R
R/methods-graph.R
R/methods-graphAM.R
R/methods-graphBAM.R
R/methods-multiGraph.R
R/nodes-methods.R
R/random.R
R/reverseEdgeDirections.R
R/settings.R
R/standardLabeling.R
R/test_graph_package.R
R/toDotWithRI.R
R/write.tlp.R
R/zzz.R
TODO
build
build/vignette.rds
data
data/MAPKsig.rda
data/apopGraph.rda
data/biocRepos.rda
data/defunctGraph.rda
data/esetsFemale.rda
data/esetsMale.rda
data/graphExamples.rda
data/integrinMediatedCellAdhesion.rda
data/pancrCaIni.rda
inst
inst/GXL
inst/GXL/attributesExample.gxl
inst/GXL/c2.gxl
inst/GXL/complexExample.gxl
inst/GXL/createGraphExamples.R
inst/GXL/graphExample-01.gxl.gz
inst/GXL/graphExample-02.gxl.gz
inst/GXL/graphExample-03.gxl.gz
inst/GXL/graphExample-04.gxl.gz
inst/GXL/graphExample-05.gxl.gz
inst/GXL/graphExample-06.gxl.gz
inst/GXL/graphExample-07.gxl.gz
inst/GXL/graphExample-08.gxl.gz
inst/GXL/graphExample-09.gxl.gz
inst/GXL/graphExample-10.gxl.gz
inst/GXL/graphExample-11.gxl.gz
inst/GXL/graphExample-12.gxl.gz
inst/GXL/graphExample-13.gxl.gz
inst/GXL/graphExample-14.gxl.gz
inst/GXL/graphExample-15.gxl.gz
inst/GXL/graphExample-16.gxl.gz
inst/GXL/graphExample-17.gxl.gz
inst/GXL/graphExample-18.gxl.gz
inst/GXL/gxl-1.0.1.dtd
inst/GXL/kmstEx.gxl
inst/GXL/outOfOrderExample.gxl
inst/GXL/simplExample.gxl.www
inst/GXL/simpleExample.gxl
inst/Scripts
inst/Scripts/Graph.R
inst/Scripts/distGraph.R
inst/Scripts/multigraph.R
inst/Scripts/pTreetest.R
inst/Scripts/testintersection.R
inst/doc
inst/doc/GraphClass.R
inst/doc/GraphClass.Rnw
inst/doc/GraphClass.pdf
inst/doc/MultiGraphClass.R
inst/doc/MultiGraphClass.Rnw
inst/doc/MultiGraphClass.pdf
inst/doc/clusterGraph.R
inst/doc/clusterGraph.Rnw
inst/doc/clusterGraph.pdf
inst/doc/graph.R
inst/doc/graph.Rnw
inst/doc/graph.pdf
inst/doc/graphAttributes.R
inst/doc/graphAttributes.Rnw
inst/doc/graphAttributes.pdf
inst/perf
inst/perf/Makefile
inst/perf/bgt.R
inst/perf/graphperf.Rnw
inst/perf/multigraphs.Rnw
inst/unitTests
inst/unitTests/MultiGraph_test.R
inst/unitTests/attrData_test.R
inst/unitTests/clusterGraph_test.R
inst/unitTests/degree_test.R
inst/unitTests/edgeWeights_test.R
inst/unitTests/graphAM_test.R
inst/unitTests/graphBAM_test.R
inst/unitTests/graphNEL_test.R
inst/unitTests/gxl_test.R
inst/unitTests/leaves_test.R
inst/unitTests/nodeAndEdgeData_test.R
inst/unitTests/setbit_test.R
inst/unitTests/simple_sparse_test.R
man
man/DFS.Rd
man/IMCA.Rd
man/MAPKsig.Rd
man/MultiGraph-class.Rd
man/acc-methods.Rd
man/addEdge.Rd
man/addNode.Rd
man/adj-methods.Rd
man/adjacencyMatrix.Rd
man/apoptosisGraph.Rd
man/attrData-class.Rd
man/attrDataItem-methods.Rd
man/attrDefaults-methods.Rd
man/aveNumEdges.Rd
man/biocRepos.Rd
man/boundary.Rd
man/calcProb.Rd
man/calcSumProb.Rd
man/clearNode.Rd
man/clusterGraph-class.Rd
man/clusteringCoefficient-methods.Rd
man/combineNodes.Rd
man/defunct.Rd
man/distGraph-class.Rd
man/duplicatedEdges.Rd
man/edgeData-methods.Rd
man/edgeDataDefaults-methods.Rd
man/edgeMatrix.Rd
man/edgeSets.Rd
man/edgeWeights.Rd
man/fromGXL-methods.Rd
man/graph-class.Rd
man/graph2SparseM.Rd
man/graphAM-class.Rd
man/graphBAM-class.Rd
man/graphExamples.Rd
man/graphNEL-class.Rd
man/inEdges.Rd
man/internal.Rd
man/isAdjacent-methods.Rd
man/isDirected-methods.Rd
man/leaves.Rd
man/listEdges.Rd
man/matrix2Graph.Rd
man/mostEdges.Rd
man/multigraph.Rd
man/nodeData-methods.Rd
man/nodeDataDefaults-methods.Rd
man/numNoEdges.Rd
man/pancrCaIni.Rd
man/randomEGraph.Rd
man/randomGraph.Rd
man/randomNodeGraph.Rd
man/removeEdge.Rd
man/removeNode.Rd
man/renderInfo-class.Rd
man/reverseEdgeDirections.Rd
man/settings.Rd
man/simpleEdge-class.Rd
man/standardLabeling.Rd
man/subGraph.Rd
man/toDotR-methods.Rd
man/toDotWithRI.Rd
man/ugraph.Rd
man/validGraph.Rd
man/write.tlp.Rd
src
src/Makevars
src/graph.c
tests
tests/graph_unit_tests.R
vignettes
vignettes/GraphClass.Rnw
vignettes/MultiGraphClass.Rnw
vignettes/clusterGraph.Rnw
vignettes/graph.Rnw
vignettes/graphAttributes.Rnw
graph documentation built on May 20, 2017, 9:32 p.m.