Bioconductor/graph
graph: A package to handle graph data structures

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Source code
53
Man pages
66
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Bioconductor/graph: graph: A package to handle graph data structures
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API

API for Bioconductor/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
.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
Bioconductor/graph documentation built on Nov. 2, 2024, 7:25 a.m.

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