graph: A package to handle graph data structures


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Documentation for package ‘graph’ version 1.72.0

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A B C D E F G I J L M N P R S T U V W misc

-- A --

acc Methods for Accessibility Lists
acc-method Methods for Accessibility Lists
acc-methods Methods for Accessibility Lists
addEdge addEdge
addEdge-method Class "graphAM"
addEdge-method EXPERIMENTAL class "graphBAM"
addEdge-method Class "graphNEL"
addNode addNode
addNode-method addNode
addNode-method Class "graphAM"
addNode-method Class "graphNEL"
adj Methods for finding the adjacency list for selected nodes.
adj-method Class "clusterGraph"
adj-method Class "distGraph"
adj-method EXPERIMENTAL class "graphBAM"
adj-method Class "graphNEL"
adj-methods Methods for finding the adjacency list for selected nodes.
adjacencyMatrix Compute an Adjacency Matrix for a graphBAM object
adjacencyMatrix-method Compute an Adjacency Matrix for a graphBAM object
aM2bpG Coercions between matrix and graph representations
apopAttrs KEGG apoptosis pathway graph
apopGraph KEGG apoptosis pathway graph
apopLocusLink KEGG apoptosis pathway graph
attrData-class Class "attrData"
attrDataItem Get and set attributes values for items in an attrData object
attrDataItem-method Class "attrData"
attrDataItem-methods Get and set attributes values for items in an attrData object
attrDataItem<- Get and set attributes values for items in an attrData object
attrDataItem<--method Class "attrData"
attrDataItem<--methods Get and set attributes values for items in an attrData object
attrDefaults Get and set the default attributes of an attrData object
attrDefaults-method Class "attrData"
attrDefaults-methods Get and set the default attributes of an attrData object
attrDefaults<- Get and set the default attributes of an attrData object
attrDefaults<--method Class "attrData"
attrDefaults<--methods Get and set the default attributes of an attrData object
aveNumEdges Calculate the average number of edges in a graph

-- B --

biocRepos A graph representing the Bioconductor package repository
boundary Returns the Boundary between a Graph and a SubGraph
buildRepDepGraph Defunct Functions in Package 'graph'

-- C --

calcProb Calculate the hypergeometric probability of the subgraph's number of edges.
calcSumProb Calculate the probability that a subgraph has an unusual number of edges.
clearNode clearNode
clearNode-method Class "graphAM"
clearNode-method EXPERIMENTAL class "graphBAM"
clearNode-method Class "graphNEL"
clusterGraph-class Class "clusterGraph"
clusteringCoefficient Clustering coefficient of a graph
clusteringCoefficient,graph Clustering coefficient of a graph
clusteringCoefficient-method Clustering coefficient of a graph
coerce Class "graphNEL"
coerce-method Class "clusterGraph"
coerce-method Class "graphAM"
coerce-method EXPERIMENTAL class "graphBAM"
coerce-method Class "graphNEL"
coerce-method Coercions between matrix and graph representations
combineNodes combineNodes
combineNodes-method combineNodes
complement Class "graph"
complement-method Class "graph"
connComp Class "graph"
connComp-method Class "clusterGraph"
connComp-method Class "graph"

-- D --

degree Class "graph"
degree-method Class "graph"
DFS Depth First Search
DFS-method Depth First Search
dfs-method Class "graph"
Dist Class "distGraph"
Dist-method Class "distGraph"
distGraph-class Class "distGraph"
dumpGXL Methods for GXL manipulations in package graph
dumpGXL-method Methods for GXL manipulations in package graph
dumpGXL-methods Methods for GXL manipulations in package graph
duplicatedEdges duplicatedEdges

-- E --

edgeData Get and set attributes for the edges of a graph object
edgeData-method Class "graph"
edgeData-method EXPERIMENTAL class "graphBAM"
edgeData-methods Get and set attributes for the edges of a graph object
edgeData<- Get and set attributes for the edges of a graph object
edgeData<--method Class "graph"
edgeData<--method EXPERIMENTAL class "graphBAM"
edgeData<--methods Get and set attributes for the edges of a graph object
edgeDataDefaults Get and set default attributes for the edges of a graph
edgeDataDefaults-method Class "graph"
edgeDataDefaults-methods Get and set default attributes for the edges of a graph
edgeDataDefaults<- Get and set default attributes for the edges of a graph
edgeDataDefaults<--method Class "graph"
edgeDataDefaults<--method EXPERIMENTAL class "graphBAM"
edgeDataDefaults<--methods Get and set default attributes for the edges of a graph
edgeL Class "graphNEL"
edgeL-method Class "clusterGraph"
edgeL-method Class "distGraph"
edgeL-method Class "graph"
edgeL-method Class "graphNEL"
edgeMatrix Compute an Edge Matrix or weight vector for a Graph
edgeMatrix-method Compute an Edge Matrix or weight vector for a Graph
edgemode Class "graph"
edgemode-method Class "graph"
edgemode-method Class "multiGraph"
edgemode<- Class "graph"
edgemode<--method Class "graph"
edgemode<--method EXPERIMENTAL class "graphBAM"
edgeNames Class "graph"
edgeNames-method EXPERIMENTAL class "MultiGraph"
edgeNames-method Class "graph"
edgeRenderInfo Class "renderInfo"
edgeRenderInfo<- Class "renderInfo"
edges Class "graphNEL"
edges-method EXPERIMENTAL class "MultiGraph"
edges-method Class "clusterGraph"
edges-method Class "distGraph"
edges-method Class "graphAM"
edges-method EXPERIMENTAL class "graphBAM"
edges-method Class "graphNEL"
edges-method Class "multiGraph"
edgeSet-class Class "multiGraph"
edgeSetAM-class Class "multiGraph"
edgeSetIntersect0 EXPERIMENTAL class "MultiGraph"
edgeSetNEL-class Class "multiGraph"
edgeSets EXPERIMENTAL class "MultiGraph"
edgeSets-method EXPERIMENTAL class "MultiGraph"
edgeSetUnion0 EXPERIMENTAL class "MultiGraph"
edgeWeights Retrieve the edge weights of a graph
edgeWeights-method Class "clusterGraph"
edgeWeights-method Class "distGraph"
edgeWeights-method Class "graph"
edgeWeights-method EXPERIMENTAL class "graphBAM"
edgeWeights-method Class "graphNEL"
esetsFemale MultiGraph edgeSet data
esetsMale MultiGraph edgeSet data
eweights EXPERIMENTAL class "MultiGraph"
eWV Compute an Edge Matrix or weight vector for a Graph
extractFromTo EXPERIMENTAL class "MultiGraph"
extractFromTo-method EXPERIMENTAL class "MultiGraph"
extractFromTo-method EXPERIMENTAL class "graphBAM"
extractGraphAM EXPERIMENTAL class "MultiGraph"
extractGraphBAM EXPERIMENTAL class "MultiGraph"

-- F --

fromGXL Methods for GXL manipulations in package graph
fromGXL-method Methods for GXL manipulations in package graph
fromGXL-methods Methods for GXL manipulations in package graph
ftM2adjM Coercions between matrix and graph representations
ftM2graphNEL Coercions between matrix and graph representations
ftM2int Standard labeling of edges with integers

-- G --

graph-class Class "graph"
graph-defunct Defunct Functions in Package 'graph'
graph.par Graphical parameters and other settings
graph.par.get Graphical parameters and other settings
graph2SparseM Coercion methods between graphs and sparse matrices
graphAM Class "graphAM"
graphAM-class Class "graphAM"
graphBAM EXPERIMENTAL class "graphBAM"
graphBAM-class EXPERIMENTAL class "graphBAM"
graphBase-class Class "graph"
graphExamples A List Of Example Graphs
graphIntersect EXPERIMENTAL class "graphBAM"
graphIntersect-method EXPERIMENTAL class "MultiGraph"
graphIntersect-method EXPERIMENTAL class "graphBAM"
graphNEL Class "graphNEL"
graphNEL-class Class "graphNEL"
graphRenderInfo Class "renderInfo"
graphRenderInfo<- Class "renderInfo"
graphUnion EXPERIMENTAL class "graphBAM"
graphUnion-method EXPERIMENTAL class "MultiGraph"
graphUnion-method EXPERIMENTAL class "graphBAM"
GXL Methods for GXL manipulations in package graph
gxlTreeNEL Methods for GXL manipulations in package graph

-- I --

IMCA KEGG Integrin Mediated Cell Adhesion graph
IMCAAttrs KEGG Integrin Mediated Cell Adhesion graph
IMCAGraph KEGG Integrin Mediated Cell Adhesion graph
inEdges Generic Method inEdges
inEdges-method Class "graphAM"
inEdges-method EXPERIMENTAL class "graphBAM"
inEdges-method Class "graphNEL"
initialize Class "graphNEL"
initialize-method Class "attrData"
initialize-method Class "distGraph"
initialize-method Class "graphAM"
initialize-method EXPERIMENTAL class "graphBAM"
initialize-method Class "graphNEL"
int2ftM Standard labeling of edges with integers
integrinMediatedCellAdhesion KEGG Integrin Mediated Cell Adhesion graph
intersection Class "graph"
intersection-method Class "graph"
intersection2 Class "graph"
intersection2-method Class "graph"
isAdjacent Determine if nodes share an edge in a graph
isAdjacent-method Class "graph"
isAdjacent-method Class "graphAM"
isAdjacent-method EXPERIMENTAL class "graphBAM"
isAdjacent-methods Determine if nodes share an edge in a graph
isConnected Class "graph"
isConnected-method Class "graph"
isDirected Determine if a graph has directed or undirected edges
isDirected-method EXPERIMENTAL class "MultiGraph"
isDirected-method Class "graph"
isDirected-method Class "multiGraph"
isDirected-methods Determine if a graph has directed or undirected edges

-- J --

join Class "graph"
join-method Class "graph"

-- L --

leaves Find the leaves of a graph
leaves-method Find the leaves of a graph
listEdges List the Edges of a Graph

-- M --

MAPKsig A graph encoding parts of the MAPK signaling pathway
mgEdgeData EXPERIMENTAL class "MultiGraph"
mgEdgeData-method EXPERIMENTAL class "MultiGraph"
mgEdgeData<- EXPERIMENTAL class "MultiGraph"
mgEdgeData<--method EXPERIMENTAL class "MultiGraph"
mgEdgeDataDefaults EXPERIMENTAL class "MultiGraph"
mgEdgeDataDefaults-method EXPERIMENTAL class "MultiGraph"
mgEdgeDataDefaults<- EXPERIMENTAL class "MultiGraph"
mgEdgeDataDefaults<--method EXPERIMENTAL class "MultiGraph"
mostEdges Find the node in a graph with the greatest number of edges
MultiGraph EXPERIMENTAL class "MultiGraph"
MultiGraph-class EXPERIMENTAL class "MultiGraph"
multiGraph-class Class "multiGraph"

-- N --

names-method Class "attrData"
names<--method Class "attrData"
NELhandler Methods for GXL manipulations in package graph
nodeData Get and set attributes for the nodes of a graph object
nodeData-method EXPERIMENTAL class "MultiGraph"
nodeData-method Class "graph"
nodeData-method EXPERIMENTAL class "graphBAM"
nodeData-methods Get and set attributes for the nodes of a graph object
nodeData<- Get and set attributes for the nodes of a graph object
nodeData<--method EXPERIMENTAL class "MultiGraph"
nodeData<--method Class "graph"
nodeData<--method EXPERIMENTAL class "graphBAM"
nodeData<--methods Get and set attributes for the nodes of a graph object
nodeDataDefaults Get and set default attributes for the nodes of a graph
nodeDataDefaults-method EXPERIMENTAL class "MultiGraph"
nodeDataDefaults-method Class "graph"
nodeDataDefaults-method EXPERIMENTAL class "graphBAM"
nodeDataDefaults-methods Get and set default attributes for the nodes of a graph
nodeDataDefaults<- Get and set default attributes for the nodes of a graph
nodeDataDefaults<--method EXPERIMENTAL class "MultiGraph"
nodeDataDefaults<--method Class "graph"
nodeDataDefaults<--method EXPERIMENTAL class "graphBAM"
nodeDataDefaults<--methods Get and set default attributes for the nodes of a graph
nodeRenderInfo Class "renderInfo"
nodeRenderInfo<- Class "renderInfo"
nodes Class "graphNEL"
nodes-method EXPERIMENTAL class "MultiGraph"
nodes-method Class "clusterGraph"
nodes-method Class "distGraph"
nodes-method Class "graph"
nodes-method Class "graphAM"
nodes-method EXPERIMENTAL class "graphBAM"
nodes-method Class "graphNEL"
nodes-method Class "multiGraph"
nodes<- Class "graphNEL"
nodes<--method Class "clusterGraph"
nodes<--method Class "graph"
nodes<--method Class "graphAM"
nodes<--method EXPERIMENTAL class "graphBAM"
nodes<--method Class "graphNEL"
numEdges Class "graph"
numEdges-method EXPERIMENTAL class "MultiGraph"
numEdges-method Class "graph"
numEdges-method Class "graphAM"
numEdges-method EXPERIMENTAL class "graphBAM"
numEdges-method Class "multiGraph"
numNodes Class "graph"
numNodes-method EXPERIMENTAL class "MultiGraph"
numNodes-method Class "clusterGraph"
numNodes-method Class "distGraph"
numNodes-method Class "graph"
numNodes-method Class "graphAM"
numNodes-method EXPERIMENTAL class "graphBAM"
numNodes-method Class "graphNEL"
numNodes-method Class "multiGraph"
numNoEdges Calculate the number of nodes that have an edge list of NULL

-- P --

pancrCaIni A graph encoding parts of the pancreatic cancer initiation pathway
parRenderInfo Class "renderInfo"
parRenderInfo<- Class "renderInfo"
pathWeights Compute an Edge Matrix or weight vector for a Graph
pkgInstOrder Defunct Functions in Package 'graph'
plot-method Class "graph"

-- R --

randomEGraph Random Edge Graph
randomGraph Random Graph
randomNodeGraph Generate Random Graph with Specified Degree Distribution
removeAttrDataItem<- Class "attrData"
removeAttrDataItem<--method Class "attrData"
removeEdge removeEdge
removeEdge-method Class "graphAM"
removeEdge-method EXPERIMENTAL class "graphBAM"
removeEdge-method Class "graphNEL"
removeEdgesByWeight EXPERIMENTAL class "graphBAM"
removeEdgesByWeight-method EXPERIMENTAL class "graphBAM"
removeNode removeNode
removeNode-method Class "graphAM"
removeNode-method EXPERIMENTAL class "graphBAM"
removeNode-method Class "graphNEL"
renderInfo-class Class "renderInfo"
reverseEdgeDirections Reverse the edges of a directed graph

-- S --

show-method EXPERIMENTAL class "MultiGraph"
show-method Class "clusterGraph"
show-method Class "distGraph"
show-method Class "graph"
show-method EXPERIMENTAL class "graphBAM"
show-method Class "multiGraph"
simpleEdge-class Class "simpleEdge".
sparseM2Graph Coercion methods between graphs and sparse matrices
subGraph Create a Subgraph
subGraph-method Create a Subgraph
subsetEdgeSets EXPERIMENTAL class "MultiGraph"

-- T --

threshold Class "distGraph"
threshold-method Class "distGraph"
toDotR Methods for Function toDotR, using R to generate a dot serialization
toDotR-method Methods for Function toDotR, using R to generate a dot serialization
toDotWithRI Translate a graph to "dot" including rendering information
toGXL Methods for GXL manipulations in package graph
toGXL-method Class "graphNEL"
toGXL-methods Methods for GXL manipulations in package graph

-- U --

ugraph Underlying Graph
ugraph-method EXPERIMENTAL class "MultiGraph"
ugraph-method EXPERIMENTAL class "graphBAM"
ugraph-method Underlying Graph
ugraphOld Defunct Functions in Package 'graph'
union-method Class "graph"
updateGraph Class "graph"
updateGraph-method Class "graph"

-- V --

validateGXL Methods for GXL manipulations in package graph
validateGXL-method Methods for GXL manipulations in package graph
validGraph Test whether graph object is valid

-- W --

write.tlp Write a graph object in a file in the Tulip format

-- misc --

[.dist Class "distGraph"