graph package - RDocumentation

adjacencyMatrix

Compute an Adjacency Matrix for a graphBAM object

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.

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

graph-defunct

Defunct Functions in Package graph

apoptosisGraph

KEGG apoptosis pathway graph

DFS

Depth First Search

integrinMediatedCellAdhesion

KEGG Integrin Mediated Cell Adhesion graph

inEdges

Generic Method inEdges

removeNode

MAPKsig

A graph encoding parts of the MAPK signaling pathway

listEdges

List the Edges of a Graph

edgeWeights

Retrieve the edge weights of a graph

renderInfo-class

Class "renderInfo"

fromGXL-methods

Methods for GXL manipulations in package graph

graphNEL-class

Class "graphNEL"

graphExamples

A List Of Example Graphs

MultiGraph-class

Class "multiGraph"

ugraph

Underlying Graph

subGraph

Create a Subgraph

toDotR-methods

Methods for Function toDotR, using R to generate a dot serialization

validGraph

Test whether graph object is valid

attrData-class

Class "attrData"

attrDataItem-methods

Get and set attributes values for items in an attrData object

clearNode

clusterGraph-class

Class "clusterGraph"

graph2SparseM

Coercion methods between graphs and sparse matrices

graph-class

Class "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

addEdge

acc-methods

Methods for Accessibility Lists

edgeSets

MultiGraph edgeSet data

edgeMatrix

Compute an Edge Matrix or weight vector for a Graph

internal

Variables used for internal purposes

isAdjacent-methods

Determine if nodes share an edge in a graph

nodeData-methods

Get and set attributes for the nodes of a graph object

reverseEdgeDirections

Reverse the edges of a directed graph

nodeDataDefaults-methods

Get and set default attributes for the nodes of a graph

graph.par

Graphical parameters and other settings

write.tlp

Write a graph object in a file in the Tulip format

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

graphAM-class

Class "graphAM"

graphBAM-class

EXPERIMENTAL class "graphBAM"

Coercions between matrix and graph representations

randomNodeGraph

Generate Random Graph with Specified Degree Distribution

mostEdges

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

removeEdge

addNode

adj-methods

Methods for finding the adjacency list for selected nodes.

clusteringCoefficient-methods

Clustering coefficient of a graph

combineNodes

distGraph-class

Class "distGraph"

duplicatedEdges

isDirected-methods

Determine if a graph has directed or undirected edges

leaves

Find the leaves of a graph

Standard labeling of edges with integers

simpleEdge-class

Class "simpleEdge".

graph (version 1.44.1)

graph: A package to handle graph data structures

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Functions in graph (1.44.1)