graph v1.50.0

graph: A package to handle graph data structures

A package that implements some simple graph handling capabilities.

Functions in graph

Name Description
acc-methods Methods for Accessibility Lists
removeNode removeNode
removeEdge removeEdge
mostEdges Find the node in a graph with the greatest number of edges
pancrCaIni A graph encoding parts of the pancreatic cancer initiation pathway
pathwayGraph Graph representing the topology of a pathway
Pathways-class Class "Pathways"
leaves Find the leaves of a graph
integrinMediatedCellAdhesion KEGG Integrin Mediated Cell Adhesion graph
calcSumProb Calculate the probability that a subgraph has an unusual number of edges.
attrData-class Class "attrData"
toDotR-methods Methods for Function toDotR, using R to generate a dot serialization
DFS Depth First Search
kegg KEGG pathways
runSPIA Run SPIA analysis
boundary Returns the Boundary between a Graph and a SubGraph
nodeDataDefaults-methods Get and set default attributes for the nodes of a graph
distGraph-class Class "distGraph"
MAPKsig A graph encoding parts of the MAPK signaling pathway
biocRepos A graph representing the Bioconductor package repository
ugraph Underlying Graph
graph2SparseM Coercion methods between graphs and sparse matrices
addNode addNode
apoptosisGraph KEGG apoptosis pathway graph
Pathway-class Class "Pathway"
multiGraph-class Class "multiGraph"
pathways Retrieve a list of pathways.
inEdges Generic Method inEdges
reactome Reactome pathways
as.list.PathwayList Convertion of PathwayLists into lists.
runTopologyGSA Run a topological analysis on an expression dataset using topologyGSA.
biocarta BioCarta pathways
humancyc Humancyc pathways
prepareSPIA Prepare pathway dataset needed by runSPIA.
validGraph Test whether graph object is valid
buildPathway Build a Pathway object.
isDirected-methods Determine if a graph has directed or undirected edges
toDotWithRI Translate a graph to "dot" including rendering information
pathwayDatabases List the available pathway databases.
combineNodes combineNodes
attrDataItem-methods Get and set attributes values for items in an attrData object
edgeMatrix Compute an Edge Matrix or weight vector for a Graph
edgeSets MultiGraph edgeSet data
attrDefaults-methods Get and set the default attributes of an attrData object
graphExamples A List Of Example Graphs
addEdge addEdge
numNoEdges Calculate the number of nodes that have an edge list of NULL
isAdjacent-methods Determine if nodes share an edge in a graph
nci NCI pathways
reverseEdgeDirections Reverse the edges of a directed graph
panther Panther pathways
convertIdentifiers Convert the node identifiers of a pathway.
aveNumEdges Calculate the average number of edges in a graph
adjacencyMatrix Compute an Adjacency Matrix for a graphBAM object
calcProb Calculate the hypergeometric probability of the subgraph's number of edges.
clearNode clearNode
graphAM-class Class "graphAM"
graphNEL-class Class "graphNEL"
write.tlp Write a graph object in a file in the Tulip format
DeprecatedPathwayList-class Class "DeprecatedPathwayList"
Standard labeling of edges with integers Standard labeling of edges with integers
renderInfo-class Class "renderInfo"
clusterGraph-class Class "clusterGraph"
graph-defunct Defunct Functions in Package graph
duplicatedEdges duplicatedEdges
edgeData-methods Get and set attributes for the edges of a graph object
edgeWeights Retrieve the edge weights of a graph
as.list.DeprecatedPathwayList Convertion of DeprecatedPathwayLists into lists.
Coercions between matrix and graph representations Coercions between matrix and graph representations
cytoscapePlot Plot a pathway graph in Cytoscape
simpleEdge-class Class "simpleEdge".
runDEGraph Run a topological analysis on an expression dataset using DEGraph package.
runClipper Run a topological analysis on an expression dataset using clipper.
runTopologyGSAMulti Run a topological analysis on an expression dataset using topologyGSA.
runDEGraphMulti Run a topological analysis on an expression dataset using DEGraph package.
adj-methods Methods for finding the adjacency list for selected nodes.
fromGXL-methods Methods for GXL manipulations in package graph
graph-class Class "graph"
edgeDataDefaults-methods Get and set default attributes for the edges of a graph
randomEGraph Random Edge Graph
PathwayList-class Class "PathwayList"
randomNodeGraph Generate Random Graph with Specified Degree Distribution
runClipperMulti Run a topological analysis on an expression dataset using clipper.
clusteringCoefficient-methods Clustering coefficient of a graph
graphBAM-class EXPERIMENTAL class "graphBAM"
listEdges List the Edges of a Graph
nodeData-methods Get and set attributes for the nodes of a graph object
randomGraph Random Graph
graph.par Graphical parameters and other settings
internal Variables used for internal purposes
subGraph Create a Subgraph
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Details

License Artistic-2.0
Collate AllClasses.R AllGenerics.R bitarray.R buildDepGraph.R methods-graph.R graphNEL.R clustergraph.R NELhandler.R edgefunctions.R graphfunctions.R GXLformals.R gxlReader.R random.R write.tlp.R mat2graph.R settings.R zzz.R standardLabeling.R TODOT.R toDotWithRI.R methods-graphAM.R attrData.R reverseEdgeDirections.R nodes-methods.R methods-multiGraph.R test_graph_package.R MultiGraph.R methods-graphBAM.R graph-constructors.R
LazyLoad yes
Packaged 2012-04-28 03:51:46 UTC; biocbuild
biocViews GraphAndNetwork

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