analyzeCluster	GOenrichment
calc.diffusion.kernel	calc.diffusion.kernel
calcICs	calcICs
calcTermSim	internal
classificationModelSignalTrans_dme	internal
classificationModelSignalTrans_hsa	internal
classificationModel_dme	internal
evaluateClustering	evaluateClustering
filterGO	filterGO
getAncestors	getAncestors
getChildren	getChildren
getDensityFactor	internal
getDepthFactor	internal
getDisjAnc	internal
getDisjCommAnc	getDisjCommAnc
getDisjCommAncSim	internal
getEnrichedSim	internal
getGeneFeatures	getGeneFeatures
getGeneFeaturesPrototypes	getGeneFeaturesPrototypes
getGeneSim	getGeneSim
getGeneSimPrototypes	getGeneSimPrototypes
getGOGraph	getGOGraph
getGOGraphsGenes	getGOGraph
getGOInfo	getGOInfo
getGSim	internal
getMinimumSubsumer	getMinimumSubsumer
getOffsprings	getOffsprings
getParents	getParents
getTermSim	getTermSim
GOenrichment	GOenrichment
GOGraph	internal
IC	IC
ICshumanBPall	IC
ICshumanCCall	IC
ICshumanMFall	IC
initialize	internal
internal	internal
load.diffusion.kernel	calc.diffusion.kernel
norm	internal
pca	internal
precomputeTermSims	internal
selectPrototypes	selectPrototypes
setEnrichmentFactors	setEnrichmentFactors
setEvidenceLevel	setEvidenceLevel
setOntology	setOntology
