graph: A package to handle graph data structures


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Documentation for package `graph' version 1.8.0

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A B C D E F G H 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,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
asGraphProperty Generic for converting input to graph property list
asGraphProperty,list,logical-method Generic for converting input to graph property list
asGraphProperty,list,missing-method Generic for converting input to graph property list
asGraphProperty,numeric,logical-method Generic for converting input to graph property list
asGraphProperty,numeric,missing-method Generic for converting input to graph property list
asGraphProperty-methods Generic for converting input to graph property list
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<-,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<-,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
bNode Class "gEdge"
bNode,gEdge-method Class "gEdge"
boundary Returns the Boundary between a Graph and a SubGraph
buildRepDepGraph Functionality to manage repository dependency graphs

-- 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,ANY-method Clustering coefficient of a graph
clusteringCoefficient,graph-method Clustering coefficient of a graph
coerce Class "graphNEL"
coerce,generalGraph-method Class "generalGraph" ~~~
coerce,graphAM,graphNEL-method Class "graphAM"
coerce,graphNEL,generalGraph-method Class "graphNEL"
coerce,graphNEL,matrix-method Coercions between matrix and graph representations
coerce,matrix,graphNEL-method Coercions between matrix and graph representations
combineNodes combineNodes
combineNodes,character,graphNEL,character-method Class "graphNEL"
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
contents Class "hashtable"
contents,hashtable,ANY-method Class "hashtable"
contents,hashtable-method Class "hashtable"

-- D --

degree Class "graph"
degree,graph,ANY-method Class "graph"
degree,graph,missing-method Class "graph"
degree,graphH,character-method Class "graphH"
degree,graphH,missing-method Class "graphH"
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<-,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<-,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
edgeID Class "gEdge"
edgeID,gEdge-method Class "gEdge"
edgeL Class "graphNEL"
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,graphNEL-method Compute an Edge Matrix or weight vector for a Graph
edgemode Class "graph"
edgemode,graph-method Class "graph"
edgemode<-,graph,character-method Class "graph"
edgeNames Class "graph"
edgeNames,graph-method Class "graph"
edgeOrder Class "gNode"
edgeOrder,gNode-method Class "gNode"
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,graphAM,character-method Class "graphAM"
edges,graphAM,missing-method Class "graphAM"
edges,graphH,character-method Class "graphH"
edges,graphH,missing-method Class "graphH"
edges,graphNEL,character-method Class "graphNEL"
edges,graphNEL,missing-method Class "graphNEL"
edgeWeights Retrieve the edge weights for specified indices.
edgeWeights,clusterGraph-method Class "clusterGraph"
edgeWeights,distGraph-method Class "distGraph"
edgeWeights,graphNEL-method Class "graphNEL"
eNode Class "gEdge"
eNode,gEdge-method Class "gEdge"
eWV Compute an Edge Matrix or weight vector for a Graph

-- F --

file-class Methods for GXL manipulations in package graph
fromEdges Class "gNode"
fromEdges,gNode-method Class "gNode"
fromEdges<-,gNode-method Class "gNode"
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 --

gEdge-class Class "gEdge"
generalGraph-class Class "generalGraph" ~~~
getNodes Class "graphH"
getNodes,graphH,character-method Class "graphH"
getNodes,graphH,missing-method Class "graphH"
gNode-class Class "gNode"
graph-class Class "graph"
graph2SparseM Coercion methods between graphs and sparse matrices
graphAM-class Class "graphAM"
graphExamples A List Of Example Graphs
graphH-class Class "graphH"
graphID-class Unique Graph Identifications
graphNEL-class Class "graphNEL"
GXL Methods for GXL manipulations in package graph
gxlTreeNEL Methods for GXL manipulations in package graph

-- H --

hash Class "hashtable"
hash,ANY,ANY,hashtable-method Class "hashtable"
hashtable Create a hashtable
hashtable-class Class "hashtable"

-- I --

idstring Class "graphH"
idstring,gEdge-method Class "gEdge"
idstring,gNode-method Class "gNode"
idstring,graphH-method Class "graphH"
IMCA KEGG Integrin Mediated Cell Adhesion graph
IMCAAttrs KEGG Integrin Mediated Cell Adhesion graph
IMCAGraph KEGG Integrin Mediated Cell Adhesion graph
inEdges inEdges
inEdges,character,graphNEL-method Class "graphNEL"
inEdges,graphNEL,missing-method inEdges
inEdges,missing,graphNEL-method Class "graphNEL"
initialize Class "graphNEL"
initialize,attrData-method Class "attrData"
initialize,distGraph-method Class "distGraph"
initialize,gEdge-method Class "gEdge"
initialize,generalGraph-method Class "generalGraph" ~~~
initialize,gNode-method Class "gNode"
initialize,graphAM-method Class "graphAM"
initialize,graphH-method Class "graphH"
initialize,graphNEL-method Class "graphNEL"
initialize,hashtable-method Class "hashtable"
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"
intersection3 Class "graph"
intersection3,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,graph-method Class "graph"
isDirected-methods Determine if a graph has directed or undirected edges

-- J --

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

-- L --

label Class "gNode"
label,gNode-method Class "gNode"
listEdges List the Edges of a Graph

-- M --

mostEdges Find the node in a graph with the greatest number of edges

-- N --

NELhandler Methods for GXL manipulations in package graph
nodeData ~~ Methods for Function nodeData in Package `graph' ~~
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 ~~ Methods for Function nodeData in Package `graph' ~~
nodeData<-,graph,character,character-method Class "graph"
nodeData<-,graph,missing,character-method Class "graph"
nodeData<--methods ~~ Methods for Function nodeData in Package `graph' ~~
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<-,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
nodeID Class "gNode"
nodeID,gNode-method Class "gNode"
nodes Class "graphNEL"
nodes,clusterGraph-method Class "clusterGraph"
nodes,distGraph-method Class "distGraph"
nodes,graphAM-method Class "graphAM"
nodes,graphH-method Class "graphH"
nodes,graphNEL-method Class "graphNEL"
nodes<-,clusterGraph,character-method Class "clusterGraph"
nodes<-,graphAM,character-method Class "graphAM"
nodes<-,graphH,character-method Class "graphH"
nodes<-,graphNEL,character-method Class "graphNEL"
nodeType Class "gNode"
nodeType,gNode-method Class "gNode"
numEdges Class "graph"
numEdges,graph-method Class "graph"
numEdges,graphAM-method Class "graphAM"
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"
numNoEdges Calculate the number of nodes that have an edge list of NULL

-- P --

pathWeights Compute an Edge Matrix or weight vector for a Graph
pkgInstOrder Functionality to manage repository dependency graphs
property Class "propertyHolder"
property,propertyHolder,character-method Class "propertyHolder"
property<-,propertyHolder,character-method Class "propertyHolder"
propertyHolder-class Class "propertyHolder"

-- R --

randomEGraph Random Edge Graph
randomGraph Random Graph
randomNodeGraph Generate a Graph with specified degree distribution.
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"

-- S --

show Class "graph"
show,clusterGraph-method Class "clusterGraph"
show,distGraph-method Class "distGraph"
show,graph-method Class "graph"
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
toEdges Class "gNode"
toEdges,gNode-method Class "gNode"
toEdges<-,gNode-method Class "gNode"
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
union Class "graph"
union,graph,graph-method Class "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"