GRAPH Interaction from pathway Topological Environment

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Documentation for package ‘graphite’ version 1.55.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

$-method	Class '"PathwayList"'
as.list.PathwayList	Convertion of PathwayLists into lists.
buildPathway	Build a Pathway object.
convertIdentifiers	Convert the node identifiers of a pathway.
convertIdentifiers-method	Class '"Pathway"'
convertIdentifiers-method	Class '"PathwayList"'
cytoscapePlot	Plot a pathway graph in Cytoscape
edges-method	Class '"Pathway"'
length-method	Class '"PathwayList"'
names-method	Class '"PathwayList"'
nodes-method	Class '"Pathway"'
Pathway-class	Class '"Pathway"'
pathwayDatabase	Class '"Pathway"'
pathwayDatabases	List the available pathway databases.
pathwayGraph	Graph representing the topology of a pathway
pathwayId	Class '"Pathway"'
PathwayList-class	Class '"PathwayList"'
pathways	Retrieve a list of pathways.
Pathways-class	Class '"Pathways"'
pathwaySpecies	Class '"Pathway"'
pathwayTimestamp	Class '"Pathway"'
pathwayTitle	Class '"Pathway"'
pathwayURL	Class '"Pathway"'
plot-method	Class '"Pathway"'
prepareSPIA	Prepare pathway dataset needed by runSPIA.
prepareSPIA-method	Class '"PathwayList"'
prepareSPIA-method	Prepare pathway dataset needed by runSPIA.
runClipper-method	Class '"Pathway"'
runClipper-method	Class '"PathwayList"'
runSPIA	Run SPIA analysis
runTopologyGSA	Run a topological analysis on an expression dataset using topologyGSA.
runTopologyGSA-method	Class '"Pathway"'
runTopologyGSA-method	Class '"PathwayList"'
runTopologyGSA-method	Run a topological analysis on an expression dataset using topologyGSA.
runTopologyGSAMulti	Run a topological analysis on an expression dataset using topologyGSA.
[-method	Class '"PathwayList"'
[[-method	Class '"PathwayList"'