# graph: A package to handle graph data structures

## Documentation for package ‘graph’ version 1.84.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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"