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MAPKsig A graph encoding parts of the MAPK signaling
pathway
MultiGraph-class EXPERIMENTAL class "MultiGraph"
aM2bpG Coercions between matrix and graph
representations
acc-methods Methods for Accessibility Lists
addEdge addEdge
addNode addNode
adj-methods Methods for finding the adjacency list for
selected nodes.
adjacencyMatrix Compute an Adjacency Matrix for a graphBAM
object
apopGraph KEGG apoptosis pathway graph
attrData-class Class "attrData"
attrDataItem-methods Get and set attributes values for items in an
attrData object
attrDefaults-methods Get and set the default attributes of an
attrData object
aveNumEdges Calculate the average number of edges in a
graph
biocRepos A graph representing the Bioconductor package
repository
boundary Returns the Boundary between a Graph and a
SubGraph
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
clusterGraph-class Class "clusterGraph"
clusteringCoefficient Clustering coefficient of a graph
combineNodes combineNodes
distGraph-class Class "distGraph"
duplicatedEdges duplicatedEdges
edgeData-methods Get and set attributes for the edges of a graph
object
edgeDataDefaults-methods
Get and set default attributes for the edges of
a graph
edgeMatrix Compute an Edge Matrix or weight vector for a
Graph
edgeWeights Retrieve the edge weights of a graph
esetsFemale MultiGraph edgeSet data
fromGXL-methods Methods for GXL manipulations in package graph
ftM2int Standard labeling of edges with integers
graph-class Class "graph"
graph-defunct Defunct Functions in Package 'graph'
graph.par Graphical parameters and other settings
graph2SparseM Coercion methods between graphs and sparse
matrices
graphAM-class Class "graphAM"
graphBAM-class EXPERIMENTAL class "graphBAM"
graphExamples A List Of Example Graphs
graphNEL-class Class "graphNEL"
inEdges Generic Method inEdges
integrinMediatedCellAdhesion
KEGG Integrin Mediated Cell Adhesion graph
isAdjacent-methods Determine if nodes share an edge in a graph
isDirected-methods Determine if a graph has directed or undirected
edges
leaves Find the leaves of a graph
listEdges List the Edges of a Graph
mostEdges Find the node in a graph with the greatest
number of edges
multiGraph-class Class "multiGraph"
nodeData-methods Get and set attributes for the nodes of a graph
object
nodeDataDefaults-methods
Get and set default attributes for the nodes of
a graph
numNoEdges Calculate the number of nodes that have an edge
list of NULL
pancrCaIni A graph encoding parts of the pancreatic cancer
initiation pathway
randomEGraph Random Edge Graph
randomGraph Random Graph
randomNodeGraph Generate Random Graph with Specified Degree
Distribution
removeEdge removeEdge
removeNode removeNode
renderInfo-class Class "renderInfo"
reverseEdgeDirections Reverse the edges of a directed graph
simpleEdge-class Class "simpleEdge".
subGraph Create a Subgraph
toDotR Methods for Function toDotR, using R to
generate a dot serialization
toDotWithRI Translate a graph to "dot" including rendering
information
ugraph Underlying Graph
validGraph Test whether graph object is valid
write.tlp Write a graph object in a file in the Tulip
format
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