NAMESPACE

export(chicagoPipeline, copyCD, defaultSettings, estimateBrownianComponent, estimateBrownianNoise, estimateDistFun, plotDistFun,
       estimateTechnicalNoise, exportResults, exportToGI, getPvals, getScores, mergeSamples, modifySettings,
       normaliseBaits, normaliseOtherEnds, plotBaits, readAndMerge, readSample, setExperiment,
       overlapFragWithFeatures, peakEnrichment4Features, chicagoData, getSkOnly)
exportMethods(intData, settings, params, "intData<-", "params<-")


import(data.table)
import(methods)
import(matrixStats)

importFrom(grDevices, dev.off, pdf)
importFrom(graphics, abline, arrows, barplot, boxplot,
           legend, lines, par, plot)
importFrom(stats, density, dist, end, lm, loess, median,
           pgamma, pnbinom, ppois, predict, quantile, sd)
importFrom(utils, read.table, write.table)
importFrom(Delaporte, pdelap)
importFrom(Hmisc, cut2)
importFrom(MASS, glm.nb, fitdistr)