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 |
.invertListOfLists | 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 |
.print_attr_list | Source code |
.print_attr_stmt | Source code |
.print_edge_stmt | Source code |
.print_node_stmt | Source code |
.print_stmt_list_fromGraph | Source code |
.print_subgraph | 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 |
.splitEdgeRenderInfo | Source code |
.splitNodeRenderInfo | Source code |
.splitRenderInfo | 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 |
.wrapAttrVal | Source code |
.wrapID | 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 |
adjacencyMatrix | Man page |
adjacencyMatrix,graphBAM-method | 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 |
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 |
coordToIndex | Source code |
degree | Man page |
degree,MultiGraph-method | Man page |
degree,graph-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 |
edges,MultiGraph-method | Man page |
edges,clusterGraph-method | Man page |
edges,distGraph-method | Man page |
edges,edgeSetAM-method | Man page |
edges,edgeSetNEL-method | Man page |
edges,graphAM-method | Man page |
edges,graphBAM-method | Man page |
edges,graphNEL-method | Man page |
edges,multiGraph-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 |
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 |
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 |
pasteq | Source code |
pathWeights | Man page |
pkgInstOrder | Man page Source code |
plot,graph,ANY-method | Man page |
plot,graph-method | Man page |
qrequire | 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,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 |
toDotWithRI | Man page Source code |
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,graph,graph-method | Man page |
updateFolder | Source code |
updateGraph | Man page |
updateGraph,graph-method | Man page |
validGraph | Man page Source code |
validateGXL | Man page |
validateGXL,connection-method | Man page |
write.tlp | Man page Source code |
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