graph: A package to handle graph data structures


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A B C D E F G H I J L M N P R S T U V W misc

-- A --

acc Methods for Accessibility Lists
acc,clusterGraph,character-method Methods for Accessibility Lists
acc,clusterGraph-method Methods for Accessibility Lists
acc,graph,character-method Methods for Accessibility Lists
acc,graph-method Methods for Accessibility Lists
acc-methods Methods for Accessibility Lists
addEdge addEdge
addEdge,character,character,graphNEL,numeric-method Class "graphNEL"
addNode addNode
addNode,character,distGraph,list-method addNode
addNode,character,graphNEL,list-method addNode
addNode,character,graphNEL,missing-method addNode
addNode,character,graphNEL-method Class "graphNEL"
adj Methods for finding the adjacency list for selected nodes.
adj,clusterGraph-method Class "clusterGraph"
adj,distGraph-method Class "distGraph"
adj,graphNEL-method Class "graphNEL"
adj-methods Methods for finding the adjacency list for selected nodes.
aM2bpG Coercing matrices to graphs
apopAttrs KEGG apoptosis pathway graph
apopGraph KEGG apoptosis pathway graph
apopLocusLink KEGG apoptosis pathway graph
aveNumEdges Calculate the average number of edges in a graph

-- B --

biocRepos A graph representing the Bioconductor package repository
bNode Class "gEdge"
bNode,gEdge-method Class "gEdge"
boundary Returns the Boundary between a Graph and a SubGraph
buildRepDepGraph Functionality to manage repository dependency graphs

-- 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,character,graphNEL-method Class "graphNEL"
clusterGraph-class Class "clusterGraph"
coerce Class "graphNEL"
coerce,generalGraph-method Class "generalGraph" ~~~
coerce,graphNEL,generalGraph-method Class "graphNEL"
coerce,graphNEL,matrix-method Coercing matrices to graphs
coerce,matrix,graphNEL-method Coercing matrices to graphs
combineNodes combineNodes
combineNodes,character,graphNEL,character-method Class "graphNEL"
complement Class "graph"
complement,graph-method Class "graph"
connComp Class "graph"
connComp,clusterGraph-method Class "clusterGraph"
connComp,graph-method Class "graph"
connection-class Methods for GXL manipulations in package graph
contents Class "hashtable"
contents,hashtable,ANY-method Class "hashtable"
contents,hashtable-method Class "hashtable"

-- D --

degree Class "graph"
degree,graph,ANY-method Class "graph"
degree,graph,missing-method Class "graph"
DFS Depth First Search
DFS,graph,character-method Depth First Search
dfs,graph-method Class "graph"
Dist Class "distGraph"
Dist,distGraph-method Class "distGraph"
distGraph-class Class "distGraph"
dumpGXL Methods for GXL manipulations in package graph
dumpGXL,connection-method Methods for GXL manipulations in package graph
dumpGXL-methods Methods for GXL manipulations in package graph
duplicatedEdges duplicatedEdges

-- E --

edgeID Class "gEdge"
edgeID,gEdge-method Class "gEdge"
edgeL Class "graphNEL"
edgeL,graphNEL-method Class "graphNEL"
edgeMatrix Compute an Edge Matrix or weight vector for a Graph
edgeMatrix,clusterGraph-method Compute an Edge Matrix or weight vector for a Graph
edgeMatrix,distGraph-method Compute an Edge Matrix or weight vector for a Graph
edgeMatrix,graphNEL-method Compute an Edge Matrix or weight vector for a Graph
edgemode Class "graph"
edgemode,graph-method Class "graph"
edgemode<-,graph,character-method Class "graph"
edgeOrder Class "gNode"
edgeOrder,gNode-method Class "gNode"
edges Class "graphNEL"
edges,clusterGraph,character-method Class "clusterGraph"
edges,clusterGraph,missing-method Class "clusterGraph"
edges,distGraph,character-method Class "distGraph"
edges,distGraph,missing-method Class "distGraph"
edges,graphNEL,character-method Class "graphNEL"
edges,graphNEL,missing-method Class "graphNEL"
edgeWeights Retrieve the edge weights for specified indices.
edgeWeights,clusterGraph-method Class "clusterGraph"
edgeWeights,distGraph-method Class "distGraph"
edgeWeights,graphNEL-method Class "graphNEL"
eNode Class "gEdge"
eNode,gEdge-method Class "gEdge"
eWV Compute an Edge Matrix or weight vector for a Graph

-- F --

file-class Methods for GXL manipulations in package graph
fromEdges Class "gNode"
fromEdges,gNode-method Class "gNode"
fromEdges<-,gNode-method Class "gNode"
fromGXL Methods for GXL manipulations in package graph
fromGXL,connection-method Methods for GXL manipulations in package graph
fromGXL-methods Methods for GXL manipulations in package graph
ftM2adjM Coercing matrices to graphs

-- G --

gEdge-class Class "gEdge"
generalGraph-class Class "generalGraph" ~~~
gNode-class Class "gNode"
graph-class Class "graph"
graph2SparseM Coercion methods between graphs and sparse matrices
graphExamples A List Of Example Graphs
graphID-class Unique Graph Identifications
graphNEL-class Class "graphNEL"
GXL Methods for GXL manipulations in package graph
gxlTreeNEL Methods for GXL manipulations in package graph

-- H --

hash Class "hashtable"
hash,ANY,ANY,hashtable-method Class "hashtable"
hashtable-class Class "hashtable"

-- I --

idenv Functions to associate identifiers with graph components.
IMCA KEGG Integrin Mediated Cell Adhesion graph
IMCAAttrs KEGG Integrin Mediated Cell Adhesion graph
IMCAGraph KEGG Integrin Mediated Cell Adhesion graph
IMCALocusLink KEGG Integrin Mediated Cell Adhesion graph
inEdges inEdges
inEdges,character,graphNEL-method Class "graphNEL"
inEdges,graphNEL,missing-method inEdges
inEdges,missing,graphNEL-method Class "graphNEL"
initialize Class "graphNEL"
initialize,generalGraph-method Class "generalGraph" ~~~
initialize,graphNEL-method Class "graphNEL"
initialize,hashtable-method Class "hashtable"
intersection Class "graph"
intersection,graph,graph-method Class "graph"
isConnected Class "graph"
isConnected,graph-method Class "graph"

-- J --

join Class "graph"
join,graph,graph-method Class "graph"

-- L --

label Class "gNode"
label,gNode-method Class "gNode"
listEdges List the Edges of a Graph

-- M --

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

-- N --

NELhandler Methods for GXL manipulations in package graph
newID Functions to associate identifiers with graph components.
nodeID Class "gNode"
nodeID,gNode-method Class "gNode"
nodes Class "graphNEL"
nodes,clusterGraph-method Class "clusterGraph"
nodes,distGraph-method Class "distGraph"
nodes,graphNEL-method Class "graphNEL"
nodes<-,graphNEL,character-method Class "graphNEL"
nodeType Class "gNode"
nodeType,gNode-method Class "gNode"
nullgraphID Functions to associate identifiers with graph components.
numEdges Calculate the number of edges in a graph
numNodes Class "graph"
numNodes,clusterGraph-method Class "clusterGraph"
numNodes,distGraph-method Class "distGraph"
numNodes,graph-method Class "graph"
numNodes,graphNEL-method Class "graphNEL"
numNoEdges Calculate the number of nodes that have an edge list of NULL

-- P --

pathWeights Compute an Edge Matrix or weight vector for a Graph
pkgInstOrder Functionality to manage repository dependency graphs

-- R --

randomEGraph Random Edge Graph
randomGraph Random Graph
randomNodeGraph Generate a Graph with specified degree distribution.
removeEdge removeEdge
removeEdge,character,character,graphNEL-method Class "graphNEL"
removeNode removeNode
removeNode,character,graphNEL-method Class "graphNEL"

-- S --

show Class "graphNEL"
show,clusterGraph-method Class "clusterGraph"
show,distGraph-method Class "distGraph"
show,graphNEL-method Class "graphNEL"
simpleEdge-class Class "simpleEdge".
sparseM2Graph Coercion methods between graphs and sparse matrices
startids Functions to associate identifiers with graph components.
subGraph Create a Subgraph
subGraph,character,clusterGraph-method Create a Subgraph
subGraph,character,distGraph-method Create a Subgraph
subGraph,character,graphNEL-method Create a Subgraph

-- T --

threshold Class "distGraph"
threshold,distGraph-method Class "distGraph"
toEdges Class "gNode"
toEdges,gNode-method Class "gNode"
toEdges<-,gNode-method Class "gNode"
toGXL Methods for GXL manipulations in package graph
toGXL,graphNEL-method Class "graphNEL"
toGXL-methods Methods for GXL manipulations in package graph

-- U --

ugraph Underlying Graph
union Class "graph"
union,graph,graph-method Class "graph"

-- V --

validateGXL Methods for GXL manipulations in package graph
validateGXL,connection-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"