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,graphNEL,numeric-method	graphNEL-class
addNode	addNode
addNode,character,distGraph,list-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-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
aveNumEdges	aveNumEdges
biocRepos	biocRepos
bNode	gEdge-class
bNode,gEdge-method	gEdge-class
boundary	boundary
buildRepDepGraph	buildRepDepGraph
calcProb	calcProb
calcSumProb	calcSumProb
clearNode	clearNode
clearNode,character,graphNEL-method	graphNEL-class
clusterGraph-class	clusterGraph-class
coerce	graphNEL-class
coerce,generalGraph-method	generalGraph-class
coerce,graphNEL,generalGraph-method	graphNEL-class
coerce,graphNEL,matrix-method	Graph2matrix
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
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
edgeID	gEdge-class
edgeID,gEdge-method	gEdge-class
edgeL	graphNEL-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
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,graphNEL,character-method	graphNEL-class
edges,graphNEL,missing-method	graphNEL-class
edgeWeights	edgeWeights
edgeWeights,clusterGraph-method	clusterGraph-class
edgeWeights,distGraph-method	distGraph-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
gEdge-class	gEdge-class
generalGraph-class	generalGraph-class
gNode-class	gNode-class
graph-class	graph-class
graph2SparseM	graph2SparseM
graphExamples	graphExamples
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-class	hashtable-class
idenv	startids
IMCA	IMCA
IMCAAttrs	IMCA
IMCAGraph	IMCA
IMCALocusLink	IMCA
inEdges	inEdges
inEdges,character,graphNEL-method	graphNEL-class
inEdges,graphNEL,missing-method	inEdges
inEdges,missing,graphNEL-method	graphNEL-class
initialize	graphNEL-class
initialize,generalGraph-method	generalGraph-class
initialize,graphNEL-method	graphNEL-class
initialize,hashtable-method	hashtable-class
intersection	graph-class
intersection,graph,graph-method	graph-class
isConnected	graph-class
isConnected,graph-method	graph-class
join	graph-class
join,graph,graph-method	graph-class
label	gNode-class
label,gNode-method	gNode-class
listEdges	listEdges
mostEdges	mostEdges
NELhandler	fromGXL-methods
newID	startids
nodeID	gNode-class
nodeID,gNode-method	gNode-class
nodes	graphNEL-class
nodes,clusterGraph-method	clusterGraph-class
nodes,distGraph-method	distGraph-class
nodes,graphNEL-method	graphNEL-class
nodes<-	graphNEL-class
nodes<-,graphNEL,character-method	graphNEL-class
nodeType	gNode-class
nodeType,gNode-method	gNode-class
nullgraphID	startids
numEdges	numEdges
numNodes	graph-class
numNodes,clusterGraph-method	clusterGraph-class
numNodes,distGraph-method	distGraph-class
numNodes,graph-method	graph-class
numNodes,graphNEL-method	graphNEL-class
numNoEdges	numNoEdges
pathWeights	edgeMatrix
pkgInstOrder	buildRepDepGraph
randomEGraph	randomEGraph
randomGraph	randomGraph
randomNodeGraph	randomNodeGraph
removeEdge	removeEdge
removeEdge,character,character,graphNEL-method	graphNEL-class
removeNode	removeNode
removeNode,character,graphNEL-method	graphNEL-class
show	graphNEL-class
show,clusterGraph-method	clusterGraph-class
show,distGraph-method	distGraph-class
show,graphNEL-method	graphNEL-class
simpleEdge-class	simpleEdge-class
sparseM2Graph	graph2SparseM
startids	startids
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
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
