import(methods)

importClassesFrom(Biobase, eSet, NChannelSet, VersionedBiobase, Versioned)
importClassesFrom(oligoClasses, TilingFeatureSet)

importMethodsFrom(oligo, pm, "pm<-", bg, "bg<-", pmindex,
	pmSequence, bgSequence, getX, getY,
	pmChr, pmPosition, probeNames, getContainer)
importMethodsFrom(BSgenome, providerVersion)
importMethodsFrom(Biobase, annotation, channelNames, rowMedians,
	sampleNames, "sampleNames<-")
importMethodsFrom(Biostrings, unmasked, vcountPattern)
importMethodsFrom(IRanges, Views)

importFrom(oligo, read.xysfiles2)
importFrom(oligoClasses, ocSamples, ocLapply,
	splitIndicesByLength, splitIndicesByNode, ldStatus, ldPath)
importFrom(preprocessCore, normalize.quantiles,
	normalize.quantiles.use.target)
importFrom(ff, ff, ffrowapply, ffcolapply, clone, clone.ff)
importFrom(Biobase, assayDataElement, "assayDataElement<-")
importFrom(Biostrings, DNAString, DNAStringSet, alphabetFrequency)
importFrom(nor1mix, norMix, qnorMix)
importFrom(siggenes, pi0.est, qvalue.cal)
importFrom(gtools, combinations)
importFrom(grDevices, dev.off, pdf, palette)
importFrom(RColorBrewer, brewer.pal)
importFrom(graphics, abline, hist, layout, legend, lines, par,
	plot, plot.new, plot.window, text)
importFrom(stats, density, dnorm, ecdf, lm, loess, loess.control,
	mad, median, na.exclude, optimize, pnorm, predict, qt, quantile,
	reshape, sd)
importFrom(utils, packageDescription, setTxtProgressBar,
	txtProgressBar)
importFrom(IRanges, nearest)
importFrom(limma, lmFit, ebayes, loessFit)
importFrom(parallel, mclapply)
importFrom(sva, sva, num.sv)


export(bgAdjust, countGC, cpgdensity, dmrFdr, dmrFinder, dmrPlot, 
	regionPlot, getControlIndex, maxDensity, pmQuality,
	methPercent, methp, normalizeBetweenSamples, normalizeWithinSamples,
	plotDensity, qcReport, readCharm, spatialAdjust, validatePd, controlQC, cmdsplot,
	dmrFind, qval, plotDMRs, plotRegions, clusterMaker, regionMatch)

# oligo exports (should we import oligo instead?)	 
export(pmindex, bgindex)
