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,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,graphNEL,list-method	addNode
addNode,character,graphNEL,missing-method	addNode
addNode,character,graphNEL-method	graphNEL-class
adj	adj-methods
adj,clusterGraph-method	clusterGraph-class
adj,distGraph-method	distGraph-class
adj,graphNEL-method	graphNEL-class
adj-methods	adj-methods
aM2bpG	matrix2Graph
apopAttrs	apoptosisGraph
apopGraph	apoptosisGraph
apopLocusLink	apoptosisGraph
asGraphProperty	asGraphProperty
asGraphProperty,list,logical-method	asGraphProperty
asGraphProperty,list,missing-method	asGraphProperty
asGraphProperty,numeric,logical-method	asGraphProperty
asGraphProperty,numeric,missing-method	asGraphProperty
asGraphProperty-methods	asGraphProperty
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
bNode	gEdge-class
bNode,gEdge-method	gEdge-class
boundary	boundary
buildRepDepGraph	buildRepDepGraph
calcProb	calcProb
calcSumProb	calcSumProb
clearNode	clearNode
clearNode,character,graphAM-method	graphAM-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,generalGraph-method	generalGraph-class
coerce,graphAM,graphNEL-method	graphAM-class
coerce,graphAM,matrix-method	graphAM-class
coerce,graphNEL,generalGraph-method	graphNEL-class
coerce,graphNEL,graphAM-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	graphNEL-class
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
contents	hashtable-class
contents,hashtable,ANY-method	hashtable-class
contents,hashtable-method	hashtable-class
degree	graph-class
degree,graph,ANY-method	graph-class
degree,graph,missing-method	graph-class
degree,graphH,character-method	graphH-class
degree,graphH,missing-method	graphH-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-methods	edgeData-methods
edgeData<-	edgeData-methods
edgeData<-,graph,character,character,character-method	graph-class
edgeData<-,graph,character,missing,character-method	graph-class
edgeData<-,graph,missing,character,character-method	graph-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-method	graph-class
edgeDataDefaults<-,graph,missing,list-method	graph-class
edgeDataDefaults<--methods	edgeDataDefaults-methods
edgeID	gEdge-class
edgeID,gEdge-method	gEdge-class
edgeL	graphNEL-class
edgeL,graph-method	graph-class
edgeL,graphNEL-method	graphNEL-class
edgeMatrix	edgeMatrix
edgeMatrix,clusterGraph-method	edgeMatrix
edgeMatrix,distGraph-method	edgeMatrix
edgeMatrix,graphNEL-method	edgeMatrix
edgemode	graph-class
edgemode,graph-method	graph-class
edgemode<-	graph-class
edgemode<-,graph,character-method	graph-class
edgeNames	graph-class
edgeNames,graph-method	graph-class
edgeOrder	gNode-class
edgeOrder,gNode-method	gNode-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,graphAM,character-method	graphAM-class
edges,graphAM,missing-method	graphAM-class
edges,graphH,character-method	graphH-class
edges,graphH,missing-method	graphH-class
edges,graphNEL,character-method	graphNEL-class
edges,graphNEL,missing-method	graphNEL-class
edgeWeights	edgeWeights
edgeWeights,clusterGraph-method	clusterGraph-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,graphNEL-method	graphNEL-class
eNode	gEdge-class
eNode,gEdge-method	gEdge-class
eWV	edgeMatrix
file-class	fromGXL-methods
fromEdges	gNode-class
fromEdges,gNode-method	gNode-class
fromEdges<-	gNode-class
fromEdges<-,gNode-method	gNode-class
fromGXL	fromGXL-methods
fromGXL,connection-method	fromGXL-methods
fromGXL-methods	fromGXL-methods
ftM2adjM	matrix2Graph
ftM2graphNEL	matrix2Graph
ftM2int	standardLabeling
gEdge-class	gEdge-class
generalGraph-class	generalGraph-class
getNodes	graphH-class
getNodes,graphH,character-method	graphH-class
getNodes,graphH,missing-method	graphH-class
gNode-class	gNode-class
graph-class	graph-class
graph2SparseM	graph2SparseM
graphAM-class	graphAM-class
graphExamples	graphExamples
graphH-class	graphH-class
graphID-class	graphID-class
graphNEL-class	graphNEL-class
GXL	fromGXL-methods
gxlTreeNEL	fromGXL-methods
hash	hashtable-class
hash,ANY,ANY,hashtable-method	hashtable-class
hashtable	hashtable
hashtable-class	hashtable-class
idstring	graphH-class
idstring,gEdge-method	gEdge-class
idstring,gNode-method	gNode-class
idstring,graphH-method	graphH-class
IMCA	IMCA
IMCAAttrs	IMCA
IMCAGraph	IMCA
inEdges	inEdges
inEdges,character,graphAM-method	graphAM-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,gEdge-method	gEdge-class
initialize,generalGraph-method	generalGraph-class
initialize,gNode-method	gNode-class
initialize,graphAM-method	graphAM-class
initialize,graphH-method	graphH-class
initialize,graphNEL-method	graphNEL-class
initialize,hashtable-method	hashtable-class
int2ftM	standardLabeling
integrinMediatedCellAdhesion	IMCA
intersection	graph-class
intersection,graph,graph-method	graph-class
intersection2	graph-class
intersection2,graph,graph-method	graph-class
intersection3	graph-class
intersection3,graph,graph-method	graph-class
isAdjacent	isAdjacent-methods
isAdjacent,graph,character,character-method	graph-class
isAdjacent,graphAM,character,character-method	graphAM-class
isAdjacent-methods	isAdjacent-methods
isConnected	graph-class
isConnected,graph-method	graph-class
isDirected	isDirected-methods
isDirected,graph-method	graph-class
isDirected-methods	isDirected-methods
join	graph-class
join,graph,graph-method	graph-class
label	gNode-class
label,gNode-method	gNode-class
listEdges	listEdges
mostEdges	mostEdges
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-methods	nodeData-methods
nodeData<-	nodeData-methods
nodeData<-,graph,character,character-method	graph-class
nodeData<-,graph,missing,character-method	graph-class
nodeData<--methods	nodeData-methods
nodeDataDefaults	nodeDataDefaults-methods
nodeDataDefaults,graph,character-method	graph-class
nodeDataDefaults,graph,missing-method	graph-class
nodeDataDefaults-methods	nodeDataDefaults-methods
nodeDataDefaults<-	nodeDataDefaults-methods
nodeDataDefaults<-,graph,character-method	graph-class
nodeDataDefaults<-,graph,missing,list-method	graph-class
nodeDataDefaults<--methods	nodeDataDefaults-methods
nodeID	gNode-class
nodeID,gNode-method	gNode-class
nodes	graphNEL-class
nodes,clusterGraph-method	clusterGraph-class
nodes,distGraph-method	distGraph-class
nodes,graphAM-method	graphAM-class
nodes,graphH-method	graphH-class
nodes,graphNEL-method	graphNEL-class
nodes<-	graphNEL-class
nodes<-,clusterGraph,character-method	clusterGraph-class
nodes<-,graphAM,character-method	graphAM-class
nodes<-,graphH,character-method	graphH-class
nodes<-,graphNEL,character-method	graphNEL-class
nodeType	gNode-class
nodeType,gNode-method	gNode-class
nullgraphID	internal
numEdges	graph-class
numEdges,graph-method	graph-class
numEdges,graphAM-method	graphAM-class
numNodes	graph-class
numNodes,clusterGraph-method	clusterGraph-class
numNodes,distGraph-method	distGraph-class
numNodes,graph-method	graph-class
numNodes,graphAM-method	graphAM-class
numNodes,graphNEL-method	graphNEL-class
numNoEdges	numNoEdges
pathWeights	edgeMatrix
pkgInstOrder	buildRepDepGraph
property	propertyHolder-class
property,propertyHolder,character-method	propertyHolder-class
property<-	propertyHolder-class
property<-,propertyHolder,character-method	propertyHolder-class
propertyHolder-class	propertyHolder-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,graphNEL-method	graphNEL-class
removeNode	removeNode
removeNode,character,graphAM-method	graphAM-class
removeNode,character,graphNEL-method	graphNEL-class
show	graph-class
show,clusterGraph-method	clusterGraph-class
show,distGraph-method	distGraph-class
show,graph-method	graph-class
simpleEdge-class	simpleEdge-class
sparseM2Graph	graph2SparseM
subGraph	subGraph
subGraph,character,clusterGraph-method	subGraph
subGraph,character,distGraph-method	subGraph
subGraph,character,graphNEL-method	subGraph
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
toEdges	gNode-class
toEdges,gNode-method	gNode-class
toEdges<-	gNode-class
toEdges<-,gNode-method	gNode-class
toGXL	fromGXL-methods
toGXL,graphNEL-method	graphNEL-class
toGXL-methods	fromGXL-methods
ugraph	ugraph
union	graph-class
union,graph,graph-method	graph-class
validateGXL	fromGXL-methods
validateGXL,connection-method	fromGXL-methods
validGraph	validGraph
write.tlp	write.tlp
[.dist	distGraph-class
