graph: A package to handle graph data structures


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Documentation for package ‘graph’ version 1.40.1

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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-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.
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'
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-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"
connection-class Methods for GXL manipulations in package 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 --

file-class Methods for GXL manipulations in package graph
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
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-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
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"
url-class Methods for GXL manipulations in package 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"