import(methods)
import(matrixStats)
importFrom(BiocGenerics, combine, updateObject, getObjectSlots)
importClassesFrom(Biobase, aggregator, container, eSet, phenoData,
                  MIAxE, MIAME, characterORMIAME,
                  annotatedDataset, AssayData, data.frameOrNULL,
                  AnnotatedDataFrame,
                  Versions, VersionsNull, Versioned, VersionedBiobase,
                  ScalarObject, ScalarInteger, ScalarLogical, ScalarNumeric,
                  ScalarCharacter)

importMethodsFrom(Biobase, "[", "[[", "$", abstract, aggenv, aggfun,
                  annotatedDataFrameFrom, annotation,
                  channel, channelNames, coerce,
                  combine, content, contents, description, dims, eList,
                  experimentData, expinfo, exprs,
                  featureNames, featureData, fData, fvarLabels, fvarMetadata,
                  geneNames, getExpData,
                  hybridizations, initfun,
                  length, locked, makeDataPackage, normControls, notes, otherInfo, pData,
                  phenoData, preproc, protocolData, sampleNames, samples, se.exprs,
                  selectChannels, snpCall, snpCallProbability, storageMode,
                  varLabels, varMetadata,
                  "annotation<-", "description<-", "dimLabels<-", "eList<-",
                  "experimentData<-", "exprs<-",
                  "featureNames<-", "featureData<-", "fData<-", "fvarLabels<-", "fvarMetadata<-",
                  "geneNames<-", "notes<-", "preproc<-", "pData<-",
                  "phenoData<-", "protocolData<-", "sampleNames<-",
                  "snpCall<-", "snpCallProbability<-", "varLabels<-",
                  "varMetadata<-", "assayData<-", "se.exprs<-",  "storageMode<-",
                  "write.exprs", dim, dimLabels, assayData, reporterNames, "reporterNames<-",
                  pubMedIds, "pubMedIds<-",
                  isVersioned, isCurrent, classVersion, "classVersion<-",
                  updateObject, updateObjectTo,
                  initialize, Compare)
import(GenomicRanges)

## including show in this import fails with obscure message during an installation
## either R CMD build (which will install the package in order to build vignette
## or by R CMD build --no-vignettes followed by R CMD INSTALL

importFrom(Biobase, assayDataElementNames,
           assayDataElement, assayDataElementReplace, "assayDataElement<-",
           "cache", "copyEnv", "copySubstitute")

importFrom(reshape, melt) 
importFrom(mclust, Mclust)
importFrom(RColorBrewer, brewer.pal)
importFrom(beanplot, beanplot)
importFrom(nor1mix, norMix, pnorMix, qnorMix)
importFrom(siggenes, pi0.est, qvalue.cal)
importFrom(limma, squeezeVar, lmFit, eBayes, contrasts.fit)
importFrom(preprocessCore, normalize.quantiles)
importFrom(crlmm, readIDAT)

export(manifestNew, getManifest, getProbeData, getProbeInfo, getManifestInfo,
       getControlAddress, getRed, getGreen, getMeth, getUnmeth,
       getBeta, getM, dmpFinder, mdsPlot, plotCpg, preprocessRaw,
       normalize.illumina.control, bgcorrect.illumina, preprocessIllumina,
       preprocessSWAN, plotBetasByType,
       detectionP, qcReport, controlStripPlot, densityBeanPlot, densityPlot,
       read.450k, read.450k.sheet, read.450k.exp, logit2, ilogit2,
       MethylSet, RGChannelSet, RGChannelSetExtended)
exportClasses(RGChannelSet, RGChannelSetExtended, MethylSet,
              IlluminaMethylationManifest, IlluminaMethylationAnnotation)
exportMethods(show, initialize)
