importClassesFrom(IRanges, CompressedIRangesList, IRanges, IRangesList, RangedData, Rle, SimpleRleList)
importClassesFrom(methods, data.frame, list, numeric)
importClassesFrom(ShortRead, AlignedRead)
importMethodsFrom(Biobase, exprs, pData, sampleNames)
importMethodsFrom(GenomicRanges, strand)
importMethodsFrom(IRanges, '%in%', as.data.frame, as.vector, cor, coverage, disjointBins, end, ifelse, levels, mean,
                  nchar, nrow, order, paste, quantile, ranges, Rle, space, start, unique, unlist, which, width)
importMethodsFrom(ShortRead, chromosome, lapply, position, sapply)
importFrom(graphics, abline, legend, lines, plot, points, rect, text)
importFrom(IRanges, IRanges, IRangesList, RangedData, RleList)
importFrom(methods, "@<-")
importFrom(ShortRead, sread)
importFrom(stats, fft, pnorm, runif)

exportMethods(export.bed, filterFFT, fragmentLenDetect, peakDetection, peakScoring, plotPeaks, processReads, controlCorrection)
export(coverage.rpm, export.wig, processTilingArray, syntheticNucMap, pcKeepCompDetect)

