acc	acc-methods
acc,clusterGraph,character-method	acc-methods
acc,clusterGraph-method	acc-methods
acc,graph,character-method	acc-methods
acc,graph-method	acc-methods
acc-methods	acc-methods
addEdge	addEdge
addEdge,character,character,graphAM,missing-method	graphAM-class
addEdge,character,character,graphBAM,missing-method	graphBAM-class
addEdge,character,character,graphBAM,numeric-method	graphBAM-class
addEdge,character,character,graphNEL,missing-method	graphNEL-class
addEdge,character,character,graphNEL,numeric-method	graphNEL-class
addNode	addNode
addNode,character,distGraph,list-method	addNode
addNode,character,graphAM,missing-method	graphAM-class
addNode,character,graphBAM,missing-method	addNode
addNode,character,graphNEL,list-method	addNode
addNode,character,graphNEL,missing-method	addNode
addNode,character,graphNEL-method	graphNEL-class
adj	adj-methods
adj,clusterGraph,ANY-method	clusterGraph-class
adj,distGraph,ANY-method	distGraph-class
adj,graphBAM,character-method	graphBAM-class
adj,graphNEL,ANY-method	graphNEL-class
adj-methods	adj-methods
aM2bpG	matrix2Graph
apopAttrs	apoptosisGraph
apopGraph	apoptosisGraph
apopLocusLink	apoptosisGraph
attrData-class	attrData-class
attrDataItem	attrDataItem-methods
attrDataItem,attrData,character,character-method	attrData-class
attrDataItem,attrData,character,missing-method	attrData-class
attrDataItem-methods	attrDataItem-methods
attrDataItem<-	attrDataItem-methods
attrDataItem<-,attrData,character,character-method	attrData-class
attrDataItem<--methods	attrDataItem-methods
attrDefaults	attrDefaults-methods
attrDefaults,attrData,character-method	attrData-class
attrDefaults,attrData,missing-method	attrData-class
attrDefaults-methods	attrDefaults-methods
attrDefaults<-	attrDefaults-methods
attrDefaults<-,attrData,character,ANY-method	attrData-class
attrDefaults<-,attrData,missing,list-method	attrData-class
attrDefaults<--methods	attrDefaults-methods
aveNumEdges	aveNumEdges
biocRepos	biocRepos
boundary	boundary
buildRepDepGraph	defunct
bzfile-class	fromGXL-methods
calcProb	calcProb
calcSumProb	calcSumProb
clearNode	clearNode
clearNode,character,graphAM-method	graphAM-class
clearNode,character,graphBAM-method	graphBAM-class
clearNode,character,graphNEL-method	graphNEL-class
clusterGraph-class	clusterGraph-class
clusteringCoefficient	clusteringCoefficient-methods
clusteringCoefficient,graph	clusteringCoefficient-methods
clusteringCoefficient,graph-method	clusteringCoefficient-methods
coerce	graphNEL-class
coerce,clusterGraph,matrix-method	clusterGraph-class
coerce,graphAM,graphBAM-method	graphAM-class
coerce,graphAM,graphNEL-method	graphAM-class
coerce,graphAM,matrix-method	graphAM-class
coerce,graphBAM,graphAM-method	graphBAM-class
coerce,graphBAM,graphNEL-method	graphBAM-class
coerce,graphBAM,matrix-method	graphBAM-class
coerce,graphNEL,generalGraph-method	graphNEL-class
coerce,graphNEL,graphAM-method	graphNEL-class
coerce,graphNEL,graphBAM-method	graphNEL-class
coerce,graphNEL,matrix-method	matrix2Graph
coerce,matrix,graphAM-method	graphAM-class
coerce,matrix,graphNEL-method	matrix2Graph
combineNodes	combineNodes
combineNodes,character,graphNEL,character-method	combineNodes
complement	graph-class
complement,graph-method	graph-class
connComp	graph-class
connComp,clusterGraph-method	clusterGraph-class
connComp,graph-method	graph-class
connection-class	fromGXL-methods
degree	graph-class
degree,graph,ANY-method	graph-class
degree,graph,missing-method	graph-class
degree,MultiGraph,missing-method	graph-class
DFS	DFS
DFS,graph,character-method	DFS
dfs,graph-method	graph-class
Dist	distGraph-class
Dist,distGraph-method	distGraph-class
distGraph-class	distGraph-class
dumpGXL	fromGXL-methods
dumpGXL,connection-method	fromGXL-methods
dumpGXL-methods	fromGXL-methods
duplicatedEdges	duplicatedEdges
edgeData	edgeData-methods
edgeData,graph,character,character,character-method	graph-class
edgeData,graph,character,character,missing-method	graph-class
edgeData,graph,character,missing,character-method	graph-class
edgeData,graph,missing,character,character-method	graph-class
edgeData,graph,missing,missing,character-method	graph-class
edgeData,graph,missing,missing,missing-method	graph-class
edgeData,graphBAM,character,character,character-method	graphBAM-class
edgeData,graphBAM,character,missing,character-method	graphBAM-class
edgeData,graphBAM,missing,character,character-method	graphBAM-class
edgeData,graphBAM,missing,missing,character-method	graphBAM-class
edgeData,graphBAM,missing,missing,missing-method	graphBAM-class
edgeData-methods	edgeData-methods
edgeData<-	edgeData-methods
edgeData<-,graph,character,character,character,ANY-method	graph-class
edgeData<-,graph,character,character,character-method	graph-class
edgeData<-,graph,character,missing,character,ANY-method	graph-class
edgeData<-,graph,character,missing,character-method	graph-class
edgeData<-,graph,missing,character,character,ANY-method	graph-class
edgeData<-,graph,missing,character,character-method	graph-class
edgeData<-,graphBAM,character,character,character,ANY-method	graphBAM-class
edgeData<-,graphBAM,character,character,character-method	graphBAM-class
edgeData<-,graphBAM,character,missing,character,ANY-method	graphBAM-class
edgeData<-,graphBAM,character,missing,character-method	graphBAM-class
edgeData<-,graphBAM,missing,character,character,ANY-method	graphBAM-class
edgeData<-,graphBAM,missing,character,character-method	graphBAM-class
edgeData<-,graphBAM,missing,missing,character,ANY-method	graphBAM-class
edgeData<-,graphBAM,missing,missing,character-method	graphBAM-class
edgeData<--methods	edgeData-methods
edgeDataDefaults	edgeDataDefaults-methods
edgeDataDefaults,graph,character-method	graph-class
edgeDataDefaults,graph,missing-method	graph-class
edgeDataDefaults-methods	edgeDataDefaults-methods
edgeDataDefaults<-	edgeDataDefaults-methods
edgeDataDefaults<-,graph,character,ANY-method	graph-class
edgeDataDefaults<-,graph,character-method	graph-class
edgeDataDefaults<-,graph,missing,list-method	graph-class
edgeDataDefaults<-,graphBAM,character,ANY-method	graphBAM-class
edgeDataDefaults<-,graphBAM,missing,list-method	graphBAM-class
edgeDataDefaults<--methods	edgeDataDefaults-methods
edgeL	graphNEL-class
edgeL,clusterGraph-method	clusterGraph-class
edgeL,distGraph-method	distGraph-class
edgeL,graph-method	graph-class
edgeL,graphNEL-method	graphNEL-class
edgeMatrix	edgeMatrix
edgeMatrix,clusterGraph-method	edgeMatrix
edgeMatrix,distGraph-method	edgeMatrix
edgeMatrix,graphAM-method	edgeMatrix
edgeMatrix,graphBAM-method	edgeMatrix
edgeMatrix,graphNEL-method	edgeMatrix
edgemode	graph-class
edgemode,edgeSet-method	multigraph
edgemode,graph-method	graph-class
edgemode<-	graph-class
edgemode<-,graph,character-method	graph-class
edgemode<-,graphBAM,character-method	graphBAM-class
edgeNames	graph-class
edgeNames,graph-method	graph-class
edgeNames,MultiGraph-method	MultiGraph-class
edgeRenderInfo	renderInfo-class
edgeRenderInfo<-	renderInfo-class
edges	graphNEL-class
edges,clusterGraph,character-method	clusterGraph-class
edges,clusterGraph,missing-method	clusterGraph-class
edges,distGraph,character-method	distGraph-class
edges,distGraph,missing-method	distGraph-class
edges,edgeSetAM,character-method	multigraph
edges,edgeSetNEL,character-method	multigraph
edges,graphAM,character-method	graphAM-class
edges,graphAM,missing-method	graphAM-class
edges,graphBAM,character-method	graphBAM-class
edges,graphBAM,missing-method	graphBAM-class
edges,graphNEL,character-method	graphNEL-class
edges,graphNEL,missing-method	graphNEL-class
edges,MultiGraph,character-method	MultiGraph-class
edges,multiGraph,character-method	multigraph
edges,MultiGraph,missing-method	MultiGraph-class
edges,multiGraph,missing-method	multigraph
edgeSet-class	multigraph
edgeSetAM-class	multigraph
edgeSetIntersect0	MultiGraph-class
edgeSetNEL-class	multigraph
edgeSets	MultiGraph-class
edgeSets,MultiGraph-method	MultiGraph-class
edgeSetUnion0	MultiGraph-class
edgeWeights	edgeWeights
edgeWeights,clusterGraph,ANY-method	clusterGraph-class
edgeWeights,clusterGraph-method	clusterGraph-class
edgeWeights,distGraph,ANY-method	distGraph-class
edgeWeights,distGraph-method	distGraph-class
edgeWeights,graph,character-method	graph-class
edgeWeights,graph,missing-method	graph-class
edgeWeights,graph,numeric-method	graph-class
edgeWeights,graphBAM,character-method	graphBAM-class
edgeWeights,graphBAM,missing-method	graphBAM-class
edgeWeights,graphBAM,numeric-method	graphBAM-class
edgeWeights,graphBAM-method	graphBAM-class
edgeWeights,graphNEL-method	graphNEL-class
esetsFemale	edgeSets
esetsMale	edgeSets
eweights	MultiGraph-class
eWV	edgeMatrix
extractFromTo	MultiGraph-class
extractFromTo,graphBAM-method	graphBAM-class
extractFromTo,MultiGraph-method	MultiGraph-class
extractGraphAM	MultiGraph-class
extractGraphBAM	MultiGraph-class
file-class	fromGXL-methods
fromGXL	fromGXL-methods
fromGXL,connection-method	fromGXL-methods
fromGXL-methods	fromGXL-methods
ftM2adjM	matrix2Graph
ftM2graphNEL	matrix2Graph
ftM2int	standardLabeling
graph-class	graph-class
graph-defunct	defunct
graph.par	settings
graph.par.get	settings
graph2SparseM	graph2SparseM
graphAM	graphAM-class
graphAM-class	graphAM-class
graphBAM	graphBAM-class
graphBAM-class	graphBAM-class
graphBase-class	graph-class
graphExamples	graphExamples
graphIntersect	graphBAM-class
graphIntersect,graphBAM,graphBAM-method	graphBAM-class
graphIntersect,MultiGraph,MultiGraph-method	MultiGraph-class
graphNEL	graphNEL-class
graphNEL-class	graphNEL-class
graphRenderInfo	renderInfo-class
graphRenderInfo<-	renderInfo-class
graphUnion	graphBAM-class
graphUnion,graphBAM,graphBAM-method	graphBAM-class
graphUnion,MultiGraph,MultiGraph-method	MultiGraph-class
GXL	fromGXL-methods
gxlTreeNEL	fromGXL-methods
gzfile-class	fromGXL-methods
IMCA	IMCA
IMCAAttrs	IMCA
IMCAGraph	IMCA
inEdges	inEdges
inEdges,character,graphAM-method	graphAM-class
inEdges,character,graphBAM-method	graphBAM-class
inEdges,character,graphNEL-method	graphNEL-class
inEdges,graphAM,missing-method	graphAM-class
inEdges,graphNEL,missing-method	graphNEL-class
inEdges,missing,graphAM-method	graphAM-class
inEdges,missing,graphNEL-method	graphNEL-class
initialize	graphNEL-class
initialize,attrData-method	attrData-class
initialize,distGraph-method	distGraph-class
initialize,graphAM-method	graphAM-class
initialize,graphBAM-method	graphBAM-class
initialize,graphNEL-method	graphNEL-class
int2ftM	standardLabeling
integrinMediatedCellAdhesion	IMCA
intersection	graph-class
intersection,graph,graph-method	graph-class
intersection2	graph-class
intersection2,graph,graph-method	graph-class
isAdjacent	isAdjacent-methods
isAdjacent,graph,character,character-method	graph-class
isAdjacent,graphAM,character,character-method	graphAM-class
isAdjacent,graphBAM,character,character-method	graphBAM-class
isAdjacent-methods	isAdjacent-methods
isConnected	graph-class
isConnected,graph-method	graph-class
isDirected	isDirected-methods
isDirected,DiEdgeSet-method	MultiGraph-class
isDirected,edgeSet-method	multigraph
isDirected,graph-method	graph-class
isDirected,MultiGraph-method	MultiGraph-class
isDirected,multiGraph-method	multigraph
isDirected,UEdgeSet-method	MultiGraph-class
isDirected-methods	isDirected-methods
join	graph-class
join,graph,graph-method	graph-class
leaves	leaves
leaves,graph-method	leaves
listEdges	listEdges
MAPKsig	MAPKsig
mgEdgeData	MultiGraph-class
mgEdgeData,MultiGraph,character,character,character,character-method	MultiGraph-class
mgEdgeData,MultiGraph,character,character,missing,character-method	MultiGraph-class
mgEdgeData,MultiGraph,character,missing,character,character-method	MultiGraph-class
mgEdgeData,MultiGraph,character,missing,missing,character-method	MultiGraph-class
mgEdgeData<-	MultiGraph-class
mgEdgeData<-,MultiGraph,character,character,character,character-method	MultiGraph-class
mgEdgeData<-,MultiGraph,character,character,missing,character-method	MultiGraph-class
mgEdgeData<-,MultiGraph,character,missing,character,character-method	MultiGraph-class
mgEdgeData<-,MultiGraph,character,missing,missing,character-method	MultiGraph-class
mgEdgeDataDefaults	MultiGraph-class
mgEdgeDataDefaults,MultiGraph,character,character-method	MultiGraph-class
mgEdgeDataDefaults,MultiGraph,character,missing-method	MultiGraph-class
mgEdgeDataDefaults<-	MultiGraph-class
mgEdgeDataDefaults<-,MultiGraph,character,character,ANY-method	MultiGraph-class
mgEdgeDataDefaults<-,MultiGraph,character,missing,list-method	MultiGraph-class
mostEdges	mostEdges
MultiGraph	MultiGraph-class
MultiGraph-class	MultiGraph-class
multiGraph-class	multigraph
names,attrData-method	attrData-class
names<-,attrData,character-method	attrData-class
NELhandler	fromGXL-methods
nodeData	nodeData-methods
nodeData,graph,character,character-method	graph-class
nodeData,graph,character,missing-method	graph-class
nodeData,graph,missing,character-method	graph-class
nodeData,graph,missing,missing-method	graph-class
nodeData,graphBAM,character,character-method	graphBAM-class
nodeData,graphBAM,character,missing-method	graphBAM-class
nodeData,graphBAM,missing,character-method	graphBAM-class
nodeData,graphBAM,missing,missing-method	graphBAM-class
nodeData,MultiGraph,character,character-method	MultiGraph-class
nodeData,MultiGraph,character,missing-method	MultiGraph-class
nodeData,MultiGraph,missing,character-method	MultiGraph-class
nodeData,MultiGraph,missing,missing-method	MultiGraph-class
nodeData-methods	nodeData-methods
nodeData<-	nodeData-methods
nodeData<-,graph,character,character-method	graph-class
nodeData<-,graph,missing,character-method	graph-class
nodeData<-,graphBAM,character,character-method	graphBAM-class
nodeData<-,graphBAM,missing,character-method	graphBAM-class
nodeData<-,MultiGraph,character,character-method	MultiGraph-class
nodeData<-,MultiGraph,missing,character-method	MultiGraph-class
nodeData<--methods	nodeData-methods
nodeDataDefaults	nodeDataDefaults-methods
nodeDataDefaults,graph,character-method	graph-class
nodeDataDefaults,graph,missing-method	graph-class
nodeDataDefaults,graphBAM,character-method	graphBAM-class
nodeDataDefaults,graphBAM,missing-method	graphBAM-class
nodeDataDefaults,MultiGraph,character-method	MultiGraph-class
nodeDataDefaults,MultiGraph,missing-method	MultiGraph-class
nodeDataDefaults-methods	nodeDataDefaults-methods
nodeDataDefaults<-	nodeDataDefaults-methods
nodeDataDefaults<-,graph,character,ANY-method	graph-class
nodeDataDefaults<-,graph,character-method	graph-class
nodeDataDefaults<-,graph,missing,list-method	graph-class
nodeDataDefaults<-,graphBAM,character,ANY-method	graphBAM-class
nodeDataDefaults<-,graphBAM,missing,ANY-method	graphBAM-class
nodeDataDefaults<-,graphBAM,missing,list-method	graphBAM-class
nodeDataDefaults<-,MultiGraph,character,ANY-method	MultiGraph-class
nodeDataDefaults<-,MultiGraph,missing,list-method	MultiGraph-class
nodeDataDefaults<--methods	nodeDataDefaults-methods
nodeRenderInfo	renderInfo-class
nodeRenderInfo<-	renderInfo-class
nodes	graphNEL-class
nodes,clusterGraph-method	clusterGraph-class
nodes,distGraph-method	distGraph-class
nodes,edgeSetAM-method	multigraph
nodes,graph-method	graph-class
nodes,graphAM-method	graphAM-class
nodes,graphBAM-method	graphBAM-class
nodes,graphNEL-method	graphNEL-class
nodes,MultiGraph-method	MultiGraph-class
nodes,multiGraph-method	multigraph
nodes<-	graphNEL-class
nodes<-,clusterGraph,character-method	clusterGraph-class
nodes<-,graph,character-method	graph-class
nodes<-,graphAM,character-method	graphAM-class
nodes<-,graphBAM,character-method	graphBAM-class
nodes<-,graphNEL,character-method	graphNEL-class
nullgraphID	internal
numEdges	graph-class
numEdges,edgeSetAM-method	multigraph
numEdges,graph-method	graph-class
numEdges,graphAM-method	graphAM-class
numEdges,graphBAM-method	graphBAM-class
numEdges,MGEdgeSet-method	MultiGraph-class
numEdges,MultiGraph-method	MultiGraph-class
numEdges,multiGraph-method	multigraph
numNodes	graph-class
numNodes,clusterGraph-method	clusterGraph-class
numNodes,distGraph-method	distGraph-class
numNodes,graph-method	graph-class
numNodes,graphAM-method	graphAM-class
numNodes,graphBAM-method	graphBAM-class
numNodes,graphNEL-method	graphNEL-class
numNodes,MultiGraph-method	MultiGraph-class
numNodes,multiGraph-method	multigraph
numNoEdges	numNoEdges
pancrCaIni	pancrCaIni
parRenderInfo	renderInfo-class
parRenderInfo<-	renderInfo-class
pathWeights	edgeMatrix
pkgInstOrder	defunct
plot,graph,ANY-method	graph-class
randomEGraph	randomEGraph
randomGraph	randomGraph
randomNodeGraph	randomNodeGraph
removeAttrDataItem<-	attrData-class
removeAttrDataItem<-,attrData,character,NULL-method	attrData-class
removeEdge	removeEdge
removeEdge,character,character,graphAM-method	graphAM-class
removeEdge,character,character,graphBAM-method	graphBAM-class
removeEdge,character,character,graphNEL-method	graphNEL-class
removeEdgesByWeight	graphBAM-class
removeEdgesByWeight,graphBAM-method	graphBAM-class
removeNode	removeNode
removeNode,character,graphAM-method	graphAM-class
removeNode,character,graphBAM-method	graphBAM-class
removeNode,character,graphNEL-method	graphNEL-class
renderInfo-class	renderInfo-class
reverseEdgeDirections	reverseEdgeDirections
show,clusterGraph-method	clusterGraph-class
show,distGraph-method	distGraph-class
show,edgeSet-method	multigraph
show,graph-method	graph-class
show,graphBAM-method	graphBAM-class
show,MultiGraph-method	MultiGraph-class
show,multiGraph-method	multigraph
simpleEdge-class	simpleEdge-class
sparseM2Graph	graph2SparseM
subGraph	subGraph
subGraph,character,clusterGraph-method	subGraph
subGraph,character,distGraph-method	subGraph
subGraph,character,graphBAM-method	subGraph
subGraph,character,graphNEL-method	subGraph
subGraph,character,MultiGraph-method	subGraph
subsetEdgeSets	MultiGraph-class
threshold	distGraph-class
threshold,distGraph-method	distGraph-class
toDotR	toDotR-methods
toDotR,graphNEL,character,list,list-method	toDotR-methods
toDotR,graphNEL,character,missing,list-method	toDotR-methods
toDotR,graphNEL,character,missing,missing-method	toDotR-methods
toDotR,graphNEL,missing,character,missing-method	toDotR-methods
toDotR,graphNEL,missing,list,list-method	toDotR-methods
toDotR,graphNEL,missing,list,missing-method	toDotR-methods
toDotR,graphNEL,missing,missing,list-method	toDotR-methods
toDotR,graphNEL,missing,missing,missing-method	toDotR-methods
toGXL	fromGXL-methods
toGXL,graphNEL-method	graphNEL-class
toGXL-methods	fromGXL-methods
ugraph	ugraph
ugraph,DiEdgeSet-method	MultiGraph-class
ugraph,graph-method	ugraph
ugraph,graphBAM-method	graphBAM-class
ugraph,MultiGraph-method	MultiGraph-class
ugraph,UEdgeSet-method	MultiGraph-class
ugraphOld	defunct
union,graph,graph-method	graph-class
updateGraph	graph-class
updateGraph,graph-method	graph-class
url-class	fromGXL-methods
validateGXL	fromGXL-methods
validateGXL,connection-method	fromGXL-methods
validGraph	validGraph
write.tlp	write.tlp
[.dist	distGraph-class
