import(BiocGenerics)
import(Biobase)


exportClasses(
    IcaSet, MineICAParams
)

exportMethods(
    dat, "dat<-", datByGene, "datByGene<-", nbComp,  organism, "organism<-", A, Alist, "A<-", S, "S<-", SByGene, "SByGene<-", SByGene, "SByGene<-",
     "[", "[<-", getComp, indComp, "indComp<-", compNames, "compNames<-", "witGenes<-", witGenes, Slist, SlistByGene, 
    chipVersion, "chipVersion<-", "chipManu<-", chipManu, "refSamples<-", refSamples, "typeID<-", typeID,
annotfile, "annotfile<-", Afile, "Afile<-", Sfile, "Sfile<-", datfile, "datfile<-", resPath, "resPath<-", genesPath, "genesPath<-", annot2col, "annot2col<-", selCutoff, "selCutoff<-", pvalCutoff, "pvalCutoff<-", geneNames, mart, "mart<-"

)

export(annot2Color)
export(annotFeatures)
export(annotFeaturesComp)
export(annotFeaturesWithBiomaRt)
export(annotInGene)
export(annotReciprocal)
export(buildIcaSet)
export(buildMineICAParams)
export(clusterFastICARuns)
export(clusterSamplesByComp)
export(clusterSamplesByComp_multiple)
export(clusVarAnalysis)
export(compareAn)
export(compareAn2graphfile)
export(compareGenes)
export(cor2An)
export(getProj)
export(getSdExpr)
export(hypergeoAn)
export(nbOccInComp)
export(nodeAttrs)
export(plotAllMix)
export(plotCorGraph)
export(plot_heatmapsOnSel)
export(plotMix)
export(plotPosAnnotInComp)
export(plotPosSamplesInComp)
export(qualVarAnalysis)
export(quantVarAnalysis)
export(relativePath)
export(runAn)
export(runCompareIcaSets)
export(runEnrich)
export(runICA)
export(selectContrib)
export(selectFeatures_IQR)
export(selectWitnessGenes)
export(writeGenes)
export(writeHtmlResTestsByAnnot)
export(writeProjByComp)
export(writeRnkFiles)