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graph (version 1.50.0)

graph: A package to handle graph data structures

Description

A package that implements some simple graph handling capabilities.

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Version

Monthly Downloads

105

Version

1.50.0

License

Artistic-2.0

Maintainer

Bioconductor Package Maintainer

Last Published

February 15th, 2017

Functions in graph (1.50.0)

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