import(methods)

#importFrom(graphics, plot)
importFrom(plyr, defaults)
importFrom(BiocGenerics, annotation)
import(S4Vectors)
importFrom(Biobase, featureNames)

exportClasses(CuffSet,
			CuffData,
			CuffDist,
			CuffFeature, 
			CuffFeatureSet, 
			CuffGene, 
			CuffGeneSet
)

exportMethods(
			runInfo,
			varModel,
			annotation,
			genes,
			isoforms,
			TSS,
			CDS,
			promoters,
			splicing,
			relCDS,
			fpkm,
			repFpkm,
			count,
			distValues,
			csDensity,
			csScatter,
			csVolcano,
			csBoxplot,
			csHeatmap,
			csFoldChangeHeatmap,
            csDistHeat,
			csCluster,
			csDendro,
			MAplot,
			dispersionPlot,
			csSpecificity,
			fpkmMatrix,
			repFpkmMatrix,
			countMatrix,
			repCountMatrix,
			diffData,
			diffTable,
			features,
			featureNames,
			samples,
			replicates,
			expressionPlot,
			expressionBarplot,
			getGene,
			getGenes,
			getFeatures,
			getGeneId,
			findGene,
			getSig,
			getSigTable,
			addFeatures,
			getLevels,
			getRepLevels,
			findSimilar,
			makeRnk,
			genePlot,
			makeGeneRegionTrack,
			DB,
			sigMatrix,
			csScatterMatrix,
			csVolcanoMatrix,
			MDSplot,
			PCAplot,
			fpkmSCVPlot,
			csNMF,
			conditions,
			csPie
)

export("readCufflinks",
		"JSdist",
		"JSdistVec",
		"JSdistFromP",
		"shannon.entropy",
		"makeprobs",
		"makeprobsvec",
		"csClusterPlot"
		)

#importClassesFrom("Biobase","Versioned")
#importClassesFrom("Biobase","VersionedBiobase")
