import(methods)
importClassesFrom(Biobase, AnnotatedDataFrame, AssayData, eSet, ExpressionSet)
importMethodsFrom(Biobase, annotation, "annotation<-", 
		assayData, "assayData<-", 
		featureData, "featureData<-", 
		featureNames, "featureNames<-",
		pData, "pData<-",
		exprs, "exprs<-",
		sampleNames, "sampleNames<-",
		coerce, combine, dim, initialize, notes, 
                storageMode, show, "[", "[[", "$")

importClassesFrom(methylumi, MethyLumiM)

importFrom(lumi, getChrInfo, getHistory, estimateBeta, m2beta, addAnnotationInfo)
importMethodsFrom(methylumi, methylated, unmethylated, "detection", "methylated<-", "unmethylated<-", "detection<-", "betas", "betas<-",  combine, "[", "dataType", "dataType<-")

importFrom(annotate, lookUp, getSYMBOL)
importFrom(AnnotationDbi, get, mget)
importFrom(genefilter, rowttests)
importFrom(biomaRt, listAttributes, getBM)

# GenoSet related classes and functions
importClassesFrom(genoset, GenoSet)
importClassesFrom(IRanges, IRanges, RangedData)
importClassesFrom(GenomicRanges, GRanges)
importMethodsFrom(IRanges, space, start, end, width, universe, values, "values<-", unlist, as.vector, as.list)
importMethodsFrom(GenomicRanges, "genome<-", "seqlengths<-", seqlevels, seqnames, "seqnames<-", "seqlevels<-", match, as.data.frame)
importMethodsFrom(genoset, locData, "locData<-", chrNames, chrInfo)
importFrom(rtracklayer, export.bw, import.bed, browserSession, ucscTableQuery, getTable, export)
importFrom(GenomicFeatures, getChromInfoFromUCSC, exons, transcripts, loadFeatures)
importFrom(IRanges, IRanges, RangedData)
importFrom(genoset, GenoSet)
importFrom(GenomicRanges, GRanges)
importFrom(Gviz, IdeogramTrack, GenomeAxisTrack, AnnotationTrack, GeneRegionTrack, BiomartGeneRegionTrack, 
	UcscTrack, DataTrack, stacks, plotTracks, coords)


exportClasses(MethyGenoSet)
exportMethods(exprs, "exprs<-", "methylated", "unmethylated", "detection", "methylated<-", "unmethylated<-", "detection<-", getHistory, combine, "[", coerce, locData, "locData<-", chrNames)

export(annotateDMRInfo, annotateGRanges, detectDMR.slideWin, export.methyGenoSet, getContinuousRegion, identifySigDMR, export.DMRInfo, MethyLumiM2GenoSet, smoothMethyData, createTranscriptTrack, buildAnnotationTracks, heatmapByChromosome, plotMethylationHeatmapByGene, plotTracksWithDataTrackInfo, checkChrName
)


