graph: A package to handle graph data structures

Documentation for package ‘graph’ version 1.24.1

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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,clusterGraph,character-method	Methods for Accessibility Lists
acc,clusterGraph-method	Methods for Accessibility Lists
acc,graph,character-method	Methods for Accessibility Lists
acc,graph-method	Methods for Accessibility Lists
acc-methods	Methods for Accessibility Lists
addEdge	addEdge
addEdge,character,character,graphAM,missing-method	Class "graphAM"
addEdge,character,character,graphNEL,missing-method	Class "graphNEL"
addEdge,character,character,graphNEL,numeric-method	Class "graphNEL"
addNode	addNode
addNode,character,distGraph,list-method	addNode
addNode,character,graphAM,missing-method	Class "graphAM"
addNode,character,graphNEL,list-method	addNode
addNode,character,graphNEL,missing-method	addNode
addNode,character,graphNEL-method	Class "graphNEL"
adj	Methods for finding the adjacency list for selected nodes.
adj,clusterGraph-method	Class "clusterGraph"
adj,distGraph-method	Class "distGraph"
adj,graphNEL-method	Class "graphNEL"
adj-methods	Methods for finding the adjacency list for selected nodes.
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,attrData,character,character-method	Class "attrData"
attrDataItem,attrData,character,missing-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<-,attrData,character,character-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,attrData,character-method	Class "attrData"
attrDefaults,attrData,missing-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<-,attrData,character,ANY-method	Class "attrData"
attrDefaults<-,attrData,missing,list-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	Functionality to manage repository dependency graphs
bzfile-class	Methods for GXL manipulations 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,character,graphAM-method	Class "graphAM"
clearNode,character,graphNEL-method	Class "graphNEL"
clusterGraph-class	Class "clusterGraph"
clusteringCoefficient	Clustering coefficient of a graph
clusteringCoefficient,graph	Clustering coefficient of a graph
clusteringCoefficient,graph-method	Clustering coefficient of a graph
coerce	Class "graphNEL"
coerce,clusterGraph,matrix-method	Class "clusterGraph"
coerce,graphAM,graphNEL-method	Class "graphAM"
coerce,graphAM,matrix-method	Class "graphAM"
coerce,graphNEL,generalGraph-method	Class "graphNEL"
coerce,graphNEL,graphAM-method	Class "graphNEL"
coerce,graphNEL,matrix-method	Coercions between matrix and graph representations
coerce,matrix,graphAM-method	Class "graphAM"
coerce,matrix,graphNEL-method	Coercions between matrix and graph representations
combineNodes	combineNodes
combineNodes,character,graphNEL,character-method	combineNodes
complement	Class "graph"
complement,graph-method	Class "graph"
connComp	Class "graph"
connComp,clusterGraph-method	Class "clusterGraph"
connComp,graph-method	Class "graph"
connection-class	Methods for GXL manipulations in package graph

-- D --

degree	Class "graph"
degree,graph,ANY-method	Class "graph"
degree,graph,missing-method	Class "graph"
DFS	Depth First Search
DFS,graph,character-method	Depth First Search
dfs,graph-method	Class "graph"
Dist	Class "distGraph"
Dist,distGraph-method	Class "distGraph"
distGraph-class	Class "distGraph"
dumpGXL	Methods for GXL manipulations in package graph
dumpGXL,connection-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,graph,character,character,character-method	Class "graph"
edgeData,graph,character,character,missing-method	Class "graph"
edgeData,graph,character,missing,character-method	Class "graph"
edgeData,graph,missing,character,character-method	Class "graph"
edgeData,graph,missing,missing,character-method	Class "graph"
edgeData,graph,missing,missing,missing-method	Class "graph"
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<-,graph,character,character,character-method	Class "graph"
edgeData<-,graph,character,missing,character-method	Class "graph"
edgeData<-,graph,missing,character,character-method	Class "graph"
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,graph,character-method	Class "graph"
edgeDataDefaults,graph,missing-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<-,graph,character,ANY-method	Class "graph"
edgeDataDefaults<-,graph,character-method	Class "graph"
edgeDataDefaults<-,graph,missing,list-method	Class "graph"
edgeDataDefaults<--methods	Get and set default attributes for the edges of a graph
edgeL	Class "graphNEL"
edgeL,clusterGraph-method	Class "clusterGraph"
edgeL,distGraph-method	Class "distGraph"
edgeL,graph-method	Class "graph"
edgeL,graphNEL-method	Class "graphNEL"
edgeMatrix	Compute an Edge Matrix or weight vector for a Graph
edgeMatrix,clusterGraph-method	Compute an Edge Matrix or weight vector for a Graph
edgeMatrix,distGraph-method	Compute an Edge Matrix or weight vector for a Graph
edgeMatrix,graphAM-method	Compute an Edge Matrix or weight vector for a Graph
edgeMatrix,graphNEL-method	Compute an Edge Matrix or weight vector for a Graph
edgemode	Class "graph"
edgemode,edgeSet-method	Class "multiGraph"
edgemode,graph-method	Class "graph"
edgemode<-	Class "graph"
edgemode<-,graph,character-method	Class "graph"
edgeNames	Class "graph"
edgeNames,graph-method	Class "graph"
edgeRenderInfo	Class "renderInfo"
edgeRenderInfo<-	Class "renderInfo"
edges	Class "graphNEL"
edges,clusterGraph,character-method	Class "clusterGraph"
edges,clusterGraph,missing-method	Class "clusterGraph"
edges,distGraph,character-method	Class "distGraph"
edges,distGraph,missing-method	Class "distGraph"
edges,edgeSetAM,character-method	Class "multiGraph"
edges,edgeSetNEL,character-method	Class "multiGraph"
edges,graphAM,character-method	Class "graphAM"
edges,graphAM,missing-method	Class "graphAM"
edges,graphNEL,character-method	Class "graphNEL"
edges,graphNEL,missing-method	Class "graphNEL"
edges,multiGraph,character-method	Class "multiGraph"
edges,multiGraph,missing-method	Class "multiGraph"
edgeSet-class	Class "multiGraph"
edgeSetAM-class	Class "multiGraph"
edgeSetNEL-class	Class "multiGraph"
edgeWeights	Retrieve the edge weights of a graph
edgeWeights,clusterGraph,ANY-method	Class "clusterGraph"
edgeWeights,clusterGraph-method	Class "clusterGraph"
edgeWeights,distGraph,ANY-method	Class "distGraph"
edgeWeights,distGraph-method	Class "distGraph"
edgeWeights,graph,character-method	Class "graph"
edgeWeights,graph,missing-method	Class "graph"
edgeWeights,graph,numeric-method	Class "graph"
edgeWeights,graphNEL-method	Class "graphNEL"
eWV	Compute an Edge Matrix or weight vector for a Graph

-- F --

file-class	Methods for GXL manipulations in package graph
fromGXL	Methods for GXL manipulations in package graph
fromGXL,connection-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.par	Graphical parameters and other settings
graph.par.get	Graphical parameters and other settings
graph2SparseM	Coercion methods between graphs and sparse matrices
graphAM-class	Class "graphAM"
graphExamples	A List Of Example Graphs
graphNEL-class	Class "graphNEL"
graphRenderInfo	Class "renderInfo"
graphRenderInfo<-	Class "renderInfo"
graphRendering	How to render a graph
GXL	Methods for GXL manipulations in package graph
gxlTreeNEL	Methods for GXL manipulations in package graph
gzfile-class	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,character,graphAM-method	Class "graphAM"
inEdges,character,graphNEL-method	Class "graphNEL"
inEdges,graphAM,missing-method	Class "graphAM"
inEdges,graphNEL,missing-method	Class "graphNEL"
inEdges,missing,graphAM-method	Class "graphAM"
inEdges,missing,graphNEL-method	Class "graphNEL"
initialize	Class "graphNEL"
initialize,attrData-method	Class "attrData"
initialize,distGraph-method	Class "distGraph"
initialize,graphAM-method	Class "graphAM"
initialize,graphNEL-method	Class "graphNEL"
int2ftM	Standard labeling of edges with integers
integrinMediatedCellAdhesion	KEGG Integrin Mediated Cell Adhesion graph
intersection	Class "graph"
intersection,graph,graph-method	Class "graph"
intersection2	Class "graph"
intersection2,graph,graph-method	Class "graph"
isAdjacent	Determine if nodes share an edge in a graph
isAdjacent,graph,character,character-method	Class "graph"
isAdjacent,graphAM,character,character-method	Class "graphAM"
isAdjacent-methods	Determine if nodes share an edge in a graph
isConnected	Class "graph"
isConnected,graph-method	Class "graph"
isDirected	Determine if a graph has directed or undirected edges
isDirected,edgeSet-method	Class "multiGraph"
isDirected,graph-method	Class "graph"
isDirected,multiGraph-method	Class "multiGraph"
isDirected-methods	Determine if a graph has directed or undirected edges

-- J --

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

-- L --

leaves	Find the leaves of a graph
leaves,graph-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
mostEdges	Find the node in a graph with the greatest number of edges
multiGraph-class	Class "multiGraph"

-- N --

names,attrData-method	Class "attrData"
names<-,attrData,character-method	Class "attrData"
NELhandler	Methods for GXL manipulations in package graph
nodeData	Get and set attributes for the nodes of a graph object
nodeData,graph,character,character-method	Class "graph"
nodeData,graph,character,missing-method	Class "graph"
nodeData,graph,missing,character-method	Class "graph"
nodeData,graph,missing,missing-method	Class "graph"
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<-,graph,character,character-method	Class "graph"
nodeData<-,graph,missing,character-method	Class "graph"
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,graph,character-method	Class "graph"
nodeDataDefaults,graph,missing-method	Class "graph"
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<-,graph,character,ANY-method	Class "graph"
nodeDataDefaults<-,graph,character-method	Class "graph"
nodeDataDefaults<-,graph,missing,list-method	Class "graph"
nodeDataDefaults<--methods	Get and set default attributes for the nodes of a graph
nodeRenderInfo	Class "renderInfo"
nodeRenderInfo<-	Class "renderInfo"
nodes	Class "graphNEL"
nodes,clusterGraph-method	Class "clusterGraph"
nodes,distGraph-method	Class "distGraph"
nodes,edgeSetAM-method	Class "multiGraph"
nodes,graph-method	Class "graph"
nodes,graphAM-method	Class "graphAM"
nodes,graphNEL-method	Class "graphNEL"
nodes,multiGraph-method	Class "multiGraph"
nodes<-	Class "graphNEL"
nodes<-,clusterGraph,character-method	Class "clusterGraph"
nodes<-,graph,character-method	Class "graph"
nodes<-,graphAM,character-method	Class "graphAM"
nodes<-,graphNEL,character-method	Class "graphNEL"
numEdges	Class "graph"
numEdges,edgeSetAM-method	Class "multiGraph"
numEdges,graph-method	Class "graph"
numEdges,graphAM-method	Class "graphAM"
numEdges,multiGraph-method	Class "multiGraph"
numNodes	Class "graph"
numNodes,clusterGraph-method	Class "clusterGraph"
numNodes,distGraph-method	Class "distGraph"
numNodes,graph-method	Class "graph"
numNodes,graphAM-method	Class "graphAM"
numNodes,graphNEL-method	Class "graphNEL"
numNodes,multiGraph-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	Functionality to manage repository dependency graphs

-- R --

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

-- S --

show	Class "graph"
show,clusterGraph-method	Class "clusterGraph"
show,distGraph-method	Class "distGraph"
show,edgeSet-method	Class "multiGraph"
show,graph-method	Class "graph"
show,multiGraph-method	Class "multiGraph"
simpleEdge-class	Class "simpleEdge".
sparseM2Graph	Coercion methods between graphs and sparse matrices
subGraph	Create a Subgraph
subGraph,character,clusterGraph-method	Create a Subgraph
subGraph,character,distGraph-method	Create a Subgraph
subGraph,character,graphNEL-method	Create a Subgraph

-- T --

threshold	Class "distGraph"
threshold,distGraph-method	Class "distGraph"
toDotR	Methods for Function toDotR, using R to generate a dot serialization
toDotR,graphNEL,character,list,list-method	Methods for Function toDotR, using R to generate a dot serialization
toDotR,graphNEL,character,missing,list-method	Methods for Function toDotR, using R to generate a dot serialization
toDotR,graphNEL,character,missing,missing-method	Methods for Function toDotR, using R to generate a dot serialization
toDotR,graphNEL,missing,character,missing-method	Methods for Function toDotR, using R to generate a dot serialization
toDotR,graphNEL,missing,list,list-method	Methods for Function toDotR, using R to generate a dot serialization
toDotR,graphNEL,missing,list,missing-method	Methods for Function toDotR, using R to generate a dot serialization
toDotR,graphNEL,missing,missing,list-method	Methods for Function toDotR, using R to generate a dot serialization
toDotR,graphNEL,missing,missing,missing-method	Methods for Function toDotR, using R to generate a dot serialization
toGXL	Methods for GXL manipulations in package graph
toGXL,graphNEL-method	Class "graphNEL"
toGXL-methods	Methods for GXL manipulations in package graph

-- U --

ugraph	Underlying Graph
ugraph,graph-method	Underlying Graph
ugraphOld	Underlying Graph
union	Class "graph"
union,graph,graph-method	Class "graph"
updateGraph	Class "graph"
updateGraph,graph-method	Class "graph"
url-class	Methods for GXL manipulations in package graph

-- V --

validateGXL	Methods for GXL manipulations in package graph
validateGXL,connection-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"