# GRAPH Interaction from pathway Topological Environment

## Documentation for package ‘graphite’ version 1.0.0

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.

## Help Pages

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"'