GRAPH Interaction from pathway Topological Environment


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Documentation for package ‘graphite’ version 1.4.0

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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
runDEGraph Run topological analysis on expression dataset using DEGraph package. See 'testOneGraph'.
runSPIA Run SPIA analysis
runTopologyGSA Run topological analysis on expression dataset using topologyGSA. See topologyGSA.
show-method Class '"pathway"'