# GRAPH Interaction from pathway Topological Environment

## Documentation for package ‘graphite’ version 1.16.0

- DESCRIPTION file.
- Package NEWS.

## Help Pages

$-method | Class '"DeprecatedPathwayList"'
$-method | Class '"PathwayList"'
as.list.DeprecatedPathwayList | Convertion of DeprecatedPathwayLists into lists.
as.list.PathwayList | Convertion of PathwayLists into lists.
biocarta | BioCarta pathways
convertIdentifiers | Convert the node identifiers of a pathway.
convertIdentifiers-method | Class '"DeprecatedPathwayList"'
convertIdentifiers-method | Class '"Pathway"'
convertIdentifiers-method | Class '"PathwayList"'
cytoscapePlot | Plot a pathway graph in Cytoscape
DeprecatedPathwayList-class | Class '"DeprecatedPathwayList"'
edges-method | Class '"Pathway"'
humancyc | Humancyc pathways
kegg | KEGG pathways
length-method | Class '"DeprecatedPathwayList"'
length-method | Class '"PathwayList"'
names-method | Class '"DeprecatedPathwayList"'
names-method | Class '"PathwayList"'
nci | NCI pathways
nodes-method | Class '"Pathway"'
panther | Panther pathways
Pathway-class | Class '"Pathway"'
pathwayDatabases | List the available pathway databases.
pathwayGraph | Graph representing the topology of a pathway
PathwayList-class | Class '"PathwayList"'
pathways | Retrieve a list of pathways.
Pathways-class | Class '"Pathways"'
plot-method | Class '"Pathway"'
prepareSPIA | Prepare pathway dataset needed by runSPIA.
prepareSPIA-method | Class '"DeprecatedPathwayList"'
prepareSPIA-method | Class '"PathwayList"'
prepareSPIA-method | Prepare pathway dataset needed by runSPIA.
reactome | Reactome pathways
runClipper | Run a topological analysis on an expression dataset using clipper.
runClipper-method | Class '"DeprecatedPathwayList"'
runClipper-method | Class '"Pathway"'
runClipper-method | Class '"PathwayList"'
runClipper-method | Run a topological analysis on an expression dataset using clipper.
runClipperMulti | Run a topological analysis on an expression dataset using clipper.
runDEGraph | Run a topological analysis on an expression dataset using DEGraph package.
runDEGraph-method | Class '"DeprecatedPathwayList"'
runDEGraph-method | Class '"Pathway"'
runDEGraph-method | Class '"PathwayList"'
runDEGraph-method | Run a topological analysis on an expression dataset using DEGraph package.
runDEGraphMulti | Run a topological analysis on an expression dataset using DEGraph package.
runSPIA | Run SPIA analysis
runTopologyGSA | Run a topological analysis on an expression dataset using topologyGSA.
runTopologyGSA-method | Class '"DeprecatedPathwayList"'
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 '"DeprecatedPathwayList"'
[-method | Class '"PathwayList"'
[[-method | Class '"DeprecatedPathwayList"'
[[-method | Class '"PathwayList"'