import(tools, Biobase)

exportClasses(SnpSetIllumina, QCIllumina)

exportMethods("[", "[[", "$", annotation, combine, experimentData, exprs, featureNames, 
             pData, phenoData, sampleNames, samples, featureData,
             "annotation<-", "description<-", "experimentData<-", "exprs<-", 
             "featureNames<-", "geneNames<-", "pData<-",
             "phenoData<-", "sampleNames<-", "assayData<-", "featureData<-",
             fData,"fData<-",
             dim, assayData, reporterNames, initialize,
             "arrayType<-", "arrayID<-", arrayType, arrayID,
             plotQC, reportSamplePanelQC,
             calculateGSR)

export("read.SnpSetIllumina", backgroundEstimate, backgroundCorrect.SNP,
       normalizeBetweenAlleles.SNP, normalizeBetweenSubsamples.SNP, 
       normalizeWithinArrays.SNP, normalizeLoci.SNP, RG2polar, polar2RG, 
       standardNormalization, heterozygousSNPs, compareGenotypes, heterozygosity, 
       reportSamplesSmoothCopyNumber, reportChromosomesSmoothCopyNumber,
       pdfSamplesSmoothCopyNumber, pdfChromosomesSmoothCopyNumber,
       removeLowQualityProbes, removeLowQualitySamples,
       calculateQCarray, pdfQC, smoothed.intensity, renameOPA,
       calculateLOH, reportGenomeGainLossLOH, pdfChromosomeGainLossLOH,
       reportChromosomeGainLossLOH, reportGenomeIntensityPlot,
       convert2aCGH, convert2SegList, segmentate, reportGenotypeSegmentation,
       plotGoldenGate4OPA, plotGenomePanels, createCNSummary, alterCN,
       getDNAindex, interactiveCNselect, setRealCN,
       Sample_Map2Samplesheet, pdfBeadstudioQC, BeadstudioQC,
       calculateLair,GetBeadStudioSampleNames, dist.GT)
