GRAPH Interaction from pathway Topological Environment


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Documentation for package ‘graphite’ version 1.24.0

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$-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
buildPathway Build a Pathway object.
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"'
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"'
pharmgkb PharmGKB 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.
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.
smpdb SMPDB pathways
[-method Class '"DeprecatedPathwayList"'
[-method Class '"PathwayList"'
[[-method Class '"DeprecatedPathwayList"'
[[-method Class '"PathwayList"'