import(BiocGenerics)
import(S4Vectors)
import(IRanges)
import(GenomeInfoDb)
import(GenomicRanges)
import(SummarizedExperiment)

import(Biobase)

importFrom(annotate,
           getAnnMap)

importMethodsFrom(AnnotationDbi,
                  mget)

importFrom(stats4, plot, summary)

importFrom(lattice,
           dotplot,
           parallel)

importFrom(GenomicFeatures,
           features)

importFrom(minfi,
           mapToGenome)

importFrom(illuminaio,
           readIDAT)

export(methylumiR, extractBarcodeAndPosition, normalizeMethyLumiSet, getAssayDataNameSubstitutions, estimateM, methylumIDAT, lumIDAT, methylumiCSV, lumiCSV, methylumi.diagnostics, qc.probe.plot, cy3, cy5, getBarcodes, stripBeadNs, stripBeadSDs, stripMethyLumiSet, psummary, negctls.stderr, methylumi.bgcorr, IDATtoMatrix, IDATsToMatrices, designItoMandU, designIItoMandU, mergeProbeDesigns, NChannelSetToMethyLumiSet, stripOOB, plotNegOob, tcgaPipeline, .mclapply)

exportClasses("MethyLumiSet","MethyLumiQC","MethyLumi", "MethyLumiM","methylData")
exportMethods("getHistory","betas","pvals","exprs","summary",
              "show","combine","hist","pairs","[",
              "QCdata","plotSampleIntensities","qcplot","total.intensity",
              "methylated","unmethylated","unmethylated<-",
              "methylated<-","QCdata<-","exprs<-","diagnostics","Cy3.N","Cy5.N",
              "pvals<-","betas<-","controlTypes","corplot", "negctls.stderr",
              "controlData", "controlData<-", "detection", "detection<-", 
              "unmethylated.N","unmethylated.N<-","pval.detect<-","pval.detect",
              "sampleNAs","probeNAs","plotNAs","normctls","negctls", 
              "methylated.N","methylated.N<-", "featureFilter","varFilter",
              "intensities.OOB","intensities.IB","negnorm","Cy3<-","Cy5<-",
              "intensities.OOB.allelic", "intensitiesByChannel","intensities.M",
              "intensities.U","combine27k450k", "dataType", "dataType<-")
