# Generated by roxygen2: do not edit by hand

export(addFeature)
export(annotateTranscripts)
export(breakTranscriptsByPeaks)
export(constructCDS)
export(constructTDS)
export(detectTranscripts)
export(estimateBackground)
export(estimateGapDistance)
export(exportCoverage)
export(getConfusionMatrix)
export(getGenomicAnnot)
export(getPeaks)
export(getPredictorSignificance)
export(getProbTreshold)
export(getQuadProb)
export(getTestedGapDistances)
export(getTranscripts)
export(peaksToBed)
export(plotErrorRate)
export(plotFeatures)
export(plotGenomicAnnot)
export(plotROC)
export(predictStrand)
export(predictTssOverlap)
export(transcriptsToBed)
exportClasses(ChipDataSet)
exportClasses(TranscriptionDataSet)
exportMethods(show)
import(GenomicRanges)
import(IRanges)
import(e1071)
import(ggplot2)
import(methods)
importClassesFrom(GenomicFeatures,TxDb)
importFrom(BiocGenerics,Reduce)
importFrom(GenomeInfoDb,keepSeqlevels)
importFrom(GenomeInfoDb,seqlevelsInUse)
importFrom(GenomicAlignments,readGAlignments)
importFrom(GenomicFeatures,exons)
importFrom(GenomicFeatures,genes)
importFrom(GenomicFeatures,intronsByTranscript)
importFrom(GenomicFeatures,promoters)
importFrom(GenomicFeatures,transcripts)
importFrom(Rsamtools,ScanBamParam)
importFrom(Rsamtools,scanBamFlag)
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,queryHits)
importFrom(S4Vectors,runValue)
importFrom(S4Vectors,subjectHits)
importFrom(caret,confusionMatrix)
importFrom(caret,createDataPartition)
importFrom(caret,train)
importFrom(caret,trainControl)
importFrom(caret,twoClassSummary)
importFrom(chipseq,peakCutoff)
importFrom(grDevices,col2rgb)
importFrom(graphics,abline)
importFrom(graphics,axis)
importFrom(graphics,legend)
importFrom(graphics,lines)
importFrom(graphics,mtext)
importFrom(graphics,par)
importFrom(graphics,plot)
importFrom(pROC,plot.roc)
importFrom(pROC,roc)
importFrom(reshape2,melt)
importFrom(rtracklayer,export)
importFrom(stats,coef)
importFrom(stats,complete.cases)
importFrom(stats,predict)
importFrom(utils,read.table)
importFrom(utils,write.table)
