ToPASeq-package	ToPASeq-package
acc,pathway,character-method	pathway-class
addEdge,character,character,pathway,numeric-method	pathway-class
addNode,character,pathway,list-method	pathway-class
AdjacencyMatrix2pathway	AdjacencyMatrix2Pathway
changeDirection	pathway-class
changeDirection,character,character,pathway,character-method	pathway-class
changeInteraction	pathway-class
changeInteraction,character,character,pathway,character,logical-method	pathway-class
clearNode,character,pathway-method	pathway-class
Clipper	Clipper
collectWeightsPRS	collectWeightsPRS
collectWeightsSPIA	collectWeightsPRS
connComp,pathway-method	pathway-class
convertIdentifiersByVector	convertIdentifiersByVector
DEGraph	DEGraph
degree,pathway,character-method	pathway-class
degree,pathway,missing-method	pathway-class
degtable	res
edgemode,pathway-method	pathway-class
edgeNames,pathway-method	pathway-class
edges,pathway,ANY-method	pathway-class
edges,pathway,character-method	pathway-class
estimateCF	estimateCF
graphNEL2pathway	graphNEL2Pathway
intersection,pathway,pathway-method	pathway-class
isAdjacent,pathway,character,character-method	pathway-class
isConnected,pathway-method	pathway-class
isDirected,pathway-method	pathway-class
join,pathway,pathway-method	pathway-class
KEGG2pathway	KEGG2pathway
makeDefaultEdgeData	defaultEdgeAttrs
mostEdges,pathway-method	pathway-class
nodes,pathway-method	pathway-class
nodes<-,pathway,character-method	pathway-class
numEdges,pathway-method	pathway-class
numNodes,pathway-method	pathway-class
numNoEdges,pathway-method	pathway-class
pathway-class	pathway-class
preparePathways	preparePathways
prepareTIF	collectWeightsPRS
PRS	PRS
PWEA	PWEA
reduceGraph	reduceRraph
removeEdge,character,character,pathway-method	pathway-class
removeNode,character,pathway-method	pathway-class
res	res
show,pathway-method	pathway-class
SPIA	SPIA
subGraph,character,pathway-method	pathway-class
TAPPA	TAPPA
ToPASeq	ToPASeq-package
topo.sig	res
TopologyGSA	TopologyGSA
union,pathway,pathway-method	pathway-class
