API for pshannon-bioc/graph
graph: A package to handle graph data structures

Global functions
.	Man page
.addDefaultAttrs	Source code
.align_from_to	Source code
.bamIntersect	Source code
.bamUnion	Source code
.checkAttrLength	Source code
.columnIndex	Source code
.coordToIndex	Source code
.createZeroBitPos	Source code
.default.graph.pars	Source code
.dropEdges	Source code
.eAttrsFun	Source code
.edgeWeight	Source code
.edges_gbam	Source code
.edges_mg	Source code
.extractFromTo_mg	Source code
.ftM2other	Source code
.getAllEdges	Source code
.getBAMIntersect	Source code
.getEdgeIntersect	Source code
.getEdgeKeys	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
.getUnionAttrs	Source code
.getUnionEdgeSet	Source code
.getUnionNodeUserAttrPos	Source code
.getUnionWeights	Source code
.get_edgeData_indicies	Source code
.indexToCoord	Source code
.makeEdgeKeys	Source code
.makeMDEdgeSet	Source code
.mgDegree	Source code
.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
.nodeDataReplaceNodeGiven	Source code
.nodeDataRetrieve	Source code
.nodeIntersect	Source code
.nodeUnion	Source code
.node_rename_check	Source code
.normalizeEdges	Source code
.onUnload	Source code
.remEdge	Source code
.rename_edge_attributes	Source code
.rename_node_attributes	Source code
.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
.rowIndex	Source code
.scaleEdgeSet	Source code
.scaleGraphBAM	Source code
.scaleMG	Source code
.scaleUserAttrPos	Source code
.set_attrs	Source code
.test	Source code
.undirectEdges	Source code
.verifyAttrListNames	Source code
.verifyAttrName	Source code
.verifyBAMAttrs	Source code
.verifyEdges	Source code
.verifyMGAttrs	Source code
.verifyMgEdgeSetNames	Source code
.verifyMgEdges	Source code
.verifyNodes	Source code
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
[.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
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
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
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
bzfile-class	Man page
calcProb	Man page Source code
calcSumProb	Man page 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
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
connection-class	Man page
coordToIndex	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
dumpGXL	Man page
dumpGXL,connection-method	Man page
dumpGXL-methods	Man page
duplicatedEdges	Man page Source code
eWV	Man page
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
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
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
extractGraphAM	Man page Source code
extractGraphBAM	Man page Source code
file-class	Man page
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
getBitCell	Source code
getColumn	Source code
getEdgeList	Source code
getIndices	Source code
getNodeIndex	Source code
getObjectSlots	Source code
getRow	Source code
getWeightList2	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
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
graphNEL-class	Man page
graphNEL_init_edgeL_weights	Source code
graphNEL_init_edges	Source code
graphNEL_init_edges_nested	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
gxlTreeNEL	Man page Source code
gzfile-class	Man page
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
makeMDEdgeSets	Source code
makebits	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
mostEdges	Man page Source code
multiGraph-class	Man page
names,attrData-method	Man page
names<-,attrData,character-method	Man page
nbitset	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
nodeRenderInfo	Man page Source code
nodeRenderInfo<-	Man page
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
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
oneWeights	Source code
pancrCaIni	Man page
parRenderInfo	Man page Source code
parRenderInfo<-	Man page
pathWeights	Man page
pkgInstOrder	Man page Source code
randFromTo	Source code
randomEGraph	Man page Source code
randomGraph	Man page Source code
randomNodeGraph	Man page 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
renderInfo-class	Man page
reverseEdgeDirections	Man page Source code
setBitCell	Source code
setRenderInfo	Source code
setbit	Source code
setbitv	Source code
show	Man page
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
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
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
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
union	Man page
union,graph,graph-method	Man page
updateFolder	Source code
updateGraph	Man page
updateGraph,graph-method	Man page
url-class	Man page
validGraph	Man page Source code
validateGXL	Man page
validateGXL,connection-method	Man page
write.tlp	Man page Source code