NAMESPACE

import(methods)
import(BiocGenerics)
import(S4Vectors)
import(SummarizedExperiment)

## Mass spec stuff

importFrom(mzR, openMSfile)
importMethodsFrom(mzR, peaks, header, close)

## "Base" packages

importFrom(Matrix, sparseMatrix)
importMethodsFrom(Matrix, crossprod)
importFrom(stats, approx, approxfun, dnorm, loess,
           model.matrix, predict)
importFrom(grDevices, colorRampPalette)

## Other packages

importFrom(IRanges, IRanges, whichAsIRanges)
importMethodsFrom(IRanges, as.matrix, cor, diff,
                  quantile, shift)

importFrom(data.table, ":=", ".N", CJ, data.table, rbindlist, setkey)
importFrom(EBImage, bwlabel)
importFrom(limma, eBayes, lmFit, topTable)

## Export

export(readMSdata, bakedpi, slicepi, CMSslice)
export(getTIC, getEICS, diffrep, plotDensityRegion)
export(densityEstimate, densityCutoff, densityQuantiles, 
       peakBounds, peakQuants)
exportClasses("CMSraw", "CMSproc", "CMSslice")
exportMethods(show, colData)