GRAPH Interaction from pathway Topological Environment

Documentation for package ‘graphite’ version 1.6.0

biocarta	BioCarta pathways
convertIdentifiers	Convert the node identifiers of a pathway.
cytoscapePlot	Plot a pathway graph in Cytoscape
edges-method	Class '"pathway"'
kegg	KEGG pathways
nci	NCI pathways
nodes-method	Class '"pathway"'
pathway-class	Class '"pathway"'
pathwayGraph	Graph representing the topology of a pathway
prepareSPIA	Prepare pathway dataset needed by runSPIA.
reactome	Reactome pathways
runClipper	Run a topological analysis on an expression dataset using the clipper.
runClipperMulti	Run topological analyses on an expression dataset, calling clipper over all the pathways in a list.
runDEGraph	Run a topological analysis on an expression dataset using DEGraph package.
runDEGraphMulti	Run topological analyses on an expression dataset, calling DEGraph over all the pathways in a list.
runSPIA	Run SPIA analysis
runTopologyGSA	Run a topological analysis on an expression dataset using topologyGSA.
runTopologyGSAMulti	Run topological analyses on an expression dataset, calling topologyGSA over all the pathways in a list.
show-method	Class '"pathway"'
spike	SPIKE pathways