import(methods)
importFrom(stats4, plot, summary)
importClassesFrom(Biobase, AnnotatedDataFrame, AssayData, eSet, ExpressionSet, Versioned, VersionedBiobase, Versions)
importMethodsFrom(Biobase, 
			    annotation, "annotation<-", 
				assayData, "assayData<-", 
			    experimentData, "experimentData<-",
			    featureData, "featureData<-", 
			    featureNames, "featureNames<-",
			    pData, "pData<-",
			    phenoData, "phenoData<-", 
				exprs, "exprs<-",
				se.exprs, "se.exprs<-",
			    sampleNames, "sampleNames<-",
				varLabels, varMetadata,
			    coerce, combine, dim, initialize, notes, storageMode, show, "[", "[[", "$")

importClassesFrom(methylumi, MethyLumi, MethyLumiSet, MethyLumiQC, MethyLumiM)
importMethodsFrom(methylumi, methylated, unmethylated, "methylated<-", "unmethylated<-", "betas", "betas<-", QCdata, combine, "[", 
 "controlData", "controlData<-", detection, "detection<-", "dataType", "dataType<-")
importFrom(methylumi, controlTypes, lumIDAT, methylumiR)

importFrom(mgcv, gam, smoothCon, mono.con, pcls, s, Predict.matrix)
importFrom(KernSmooth, locpoly)
importFrom(lattice, bwplot, panel.violin)
importFrom(nleqslv, nleqslv)
importFrom(annotate, lookUp, getSYMBOL)
importClassesFrom(RSQLite, SQLiteDriver, SQLiteConnection)
importMethodsFrom(RSQLite, dbReadTable, dbListTables, dbConnect, dbDisconnect, dbListFields)
importFrom(DBI, dbReadTable, dbListTables, dbConnect, dbDisconnect, dbListFields, dbDriver, dbDataType, dbCommit, dbClearResult, SQLKeywords)

importFrom(AnnotationDbi, as.list)
importClassesFrom(AnnotationDbi, AnnDbBimap)
importMethodsFrom(AnnotationDbi, "[", mappedkeys)

importFrom(graphics, pairs, boxplot, hist, image, lines, matplot, points, abline, axis, par, text)
importFrom(stats, density, heatmap)
importFrom(MASS, rlm, psi.bisquare)
importFrom(affy, normalize.loess, mva.pairs, bg.adjust, plotDensity)
importFrom(preprocessCore, normalize.quantiles, normalize.quantiles.robust)

importFrom(GenomicFeatures, features)
importFrom(GenomicRanges, seqnames)


exportClasses(LumiBatch)
exportMethods(beadNum, "beadNum<-", boxplot, combine, density, detection, "detection<-", getHistory, hist, MAplot, pairs, plot, "sampleNames<-", exprs, "exprs<-", se.exprs, "se.exprs<-", show, summary, "[", coerce, "controlData", "controlData<-", asBigMatrix)

export(IlluminaID2nuID, addControlData2lumi, addNuID2lumi, addNuId2lumi,                                                            
bgAdjust, detectOutlier, detectionCall, estimateLumiCV, getChipInfo, getControlData, getControlProbe,
getControlType, getNuIDMappingInfo, id2seq, inverseVST, is.nuID, lumiB, lumiExpresso, lumiN, lumiQ,                       
lumiR, lumiR.batch, lumiT, nuID2EntrezID, nuID2IlluminaID, nuID2RefSeqID, nuID2probeID, nuID2targetID,
plotCDF, plotControlData, plotDensity, plotHousekeepingGene, plotSampleRelation, plotStringencyGene, plotVST, probeID2nuID,
produceGEOPlatformFile, produceGEOSampleInfoTemplate, produceGEOSubmissionFile, rsn, seq2id, ssn, targetID2nuID, vst, rankinvariant,
addAnnotationInfo, addControlData2methyLumiM, adjColorBias.quantile, adjColorBias.ssn, beta2m, bgAdjustMethylation, boxplotColorBias, colorBiasSummary, estimateBeta, estimateM,
estimateIntensity, estimateMethylationBG, importMethyIDAT, lumiMethyB, lumiMethyC, lumiMethyN, lumiMethyR, m2beta, normalizeMethylation.quantile, 
normalizeMethylation.ssn, plotColorBias2D, plotColorBias1D, produceMethylationGEOSubmissionFile, smoothQuantileNormalization, 
lumiMethyStatus, gammaFitEM, methylationCall, plotGammaFit, getChrInfo
)


