# Generated by roxygen2: do not edit by hand

S3method(fit,FraserDataSet)
export("bamFile<-")
export("condition<-")
export("currentType<-")
export("dontWriteHDF5<-")
export("featureExclusionMask<-")
export("fitMetrics<-")
export("name<-")
export("nonSplicedReads<-")
export("pairedEnd<-")
export("samples<-")
export("scanBamParam<-")
export("strandSpecific<-")
export("verbose<-")
export("workingDir<-")
export(FRASER)
export(FRASER.mcols.get)
export(FRASER.rowRanges.get)
export(FraserDataSet)
export(K)
export(N)
export(aberrant)
export(addCountsToFraserDataSet)
export(annotateIntronReferenceOverlap)
export(annotatePotentialImpact)
export(annotateRanges)
export(annotateRangesWithTxDb)
export(availableFDRsubsets)
export(bamFile)
export(bestQ)
export(calculatePSIValues)
export(calculatePadjValues)
export(calculatePadjValuesOnSubset)
export(calculatePvalues)
export(calculateZscore)
export(condition)
export(countNonSplicedReads)
export(countRNAData)
export(countSplitReads)
export(createTestFraserDataSet)
export(createTestFraserSettings)
export(currentType)
export(deltaPsiValue)
export(dontWriteHDF5)
export(estimateBestQ)
export(featureExclusionMask)
export(filterExpression)
export(filterExpressionAndVariability)
export(filterVariability)
export(fit)
export(fitMetrics)
export(flagBlacklistRegions)
export(getNonSplitReadCountsForAllSamples)
export(getSplitReadCountsForAllSamples)
export(hyperParams)
export(injectOutliers)
export(loadFraserDataSet)
export(makeSimulatedFraserDataSet)
export(mapSeqlevels)
export(mergeCounts)
export(mergeExternalData)
export(name)
export(nonSplicedReads)
export(pVals)
export(padjVals)
export(pairedEnd)
export(plotAberrantPerSample)
export(plotBamCoverage)
export(plotBamCoverageFromResultTable)
export(plotCountCorHeatmap)
export(plotEncDimSearch)
export(plotExpectedVsObservedPsi)
export(plotExpression)
export(plotFilterExpression)
export(plotFilterVariability)
export(plotManhattan)
export(plotQQ)
export(plotSpliceMetricRank)
export(plotVolcano)
export(predictedMeans)
export(pseudocount)
export(psiTypes)
export(results)
export(rho)
export(samples)
export(saveFraserDataSet)
export(scanBamParam)
export(strandSpecific)
export(verbose)
export(workingDir)
export(zScores)
exportMethods("[")
exportMethods("assays<-")
exportMethods("bamFile<-")
exportMethods("condition<-")
exportMethods("name<-")
exportMethods("nonSplicedReads<-")
exportMethods("pairedEnd<-")
exportMethods("samples<-")
exportMethods("scanBamParam<-")
exportMethods("strandSpecific<-")
exportMethods("workingDir<-")
exportMethods(aberrant)
exportMethods(assayNames)
exportMethods(assays)
exportMethods(bamFile)
exportMethods(condition)
exportMethods(filterExpression)
exportMethods(filterVariability)
exportMethods(length)
exportMethods(name)
exportMethods(nonSplicedReads)
exportMethods(pairedEnd)
exportMethods(plotAberrantPerSample)
exportMethods(plotCountCorHeatmap)
exportMethods(plotEncDimSearch)
exportMethods(plotManhattan)
exportMethods(plotQQ)
exportMethods(plotVolcano)
exportMethods(results)
exportMethods(samples)
exportMethods(scanBamParam)
exportMethods(strandSpecific)
exportMethods(workingDir)
import(BiocParallel)
import(data.table)
importFrom(AnnotationDbi,select)
importFrom(BBmisc,"%nin%")
importFrom(BBmisc,chunk)
importFrom(BBmisc,is.error)
importFrom(BBmisc,isFALSE)
importFrom(BBmisc,isScalarCharacter)
importFrom(BBmisc,isScalarInteger)
importFrom(BBmisc,isScalarLogical)
importFrom(BBmisc,isScalarNumeric)
importFrom(BBmisc,isScalarValue)
importFrom(BBmisc,seq_col)
importFrom(BBmisc,seq_row)
importFrom(BSgenome,getBSgenome)
importFrom(Biobase,rowMax)
importFrom(BiocGenerics,"counts<-")
importFrom(BiocGenerics,"strand<-")
importFrom(BiocGenerics,counts)
importFrom(BiocGenerics,strand)
importFrom(BiocGenerics,updateObject)
importFrom(BiocGenerics,which)
importFrom(DelayedArray,"path<-")
importFrom(DelayedArray,DelayedArray)
importFrom(DelayedArray,cbind)
importFrom(DelayedArray,plogis)
importFrom(DelayedArray,qlogis)
importFrom(DelayedArray,rowMaxs)
importFrom(DelayedArray,rowMeans)
importFrom(DelayedMatrixStats,colMeans2)
importFrom(DelayedMatrixStats,colSds)
importFrom(DelayedMatrixStats,rowMeans2)
importFrom(DelayedMatrixStats,rowMedians)
importFrom(DelayedMatrixStats,rowQuantiles)
importFrom(DelayedMatrixStats,rowSds)
importFrom(GenomeInfoDb,"seqlengths<-")
importFrom(GenomeInfoDb,"seqlevels<-")
importFrom(GenomeInfoDb,"seqlevelsStyle<-")
importFrom(GenomeInfoDb,dropSeqlevels)
importFrom(GenomeInfoDb,keepSeqlevels)
importFrom(GenomeInfoDb,keepStandardChromosomes)
importFrom(GenomeInfoDb,seqinfo)
importFrom(GenomeInfoDb,seqlengths)
importFrom(GenomeInfoDb,seqlevels)
importFrom(GenomeInfoDb,seqlevelsStyle)
importFrom(GenomeInfoDb,seqnames)
importFrom(GenomeInfoDb,sortSeqlevels)
importFrom(GenomeInfoDb,standardChromosomes)
importFrom(GenomicAlignments,junctions)
importFrom(GenomicAlignments,readGAlignmentPairs)
importFrom(GenomicAlignments,readGAlignments)
importFrom(GenomicAlignments,summarizeJunctions)
importFrom(GenomicFeatures,exons)
importFrom(GenomicFeatures,fiveUTRsByTranscript)
importFrom(GenomicFeatures,genes)
importFrom(GenomicFeatures,intronsByTranscript)
importFrom(GenomicFeatures,seqlevels0)
importFrom(GenomicFeatures,threeUTRsByTranscript)
importFrom(GenomicRanges,"end<-")
importFrom(GenomicRanges,"seqinfo<-")
importFrom(GenomicRanges,"start<-")
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,GRangesList)
importFrom(GenomicRanges,end)
importFrom(GenomicRanges,findOverlaps)
importFrom(GenomicRanges,granges)
importFrom(GenomicRanges,invertStrand)
importFrom(GenomicRanges,makeGRangesFromDataFrame)
importFrom(GenomicRanges,start)
importFrom(HDF5Array,HDF5Array)
importFrom(HDF5Array,loadHDF5SummarizedExperiment)
importFrom(HDF5Array,path)
importFrom(HDF5Array,saveHDF5SummarizedExperiment)
importFrom(HDF5Array,writeHDF5Array)
importFrom(IRanges,"%over%")
importFrom(IRanges,IRanges)
importFrom(IRanges,distance)
importFrom(IRanges,from)
importFrom(IRanges,nearest)
importFrom(IRanges,ranges)
importFrom(IRanges,subsetByOverlaps)
importFrom(IRanges,to)
importFrom(OUTRIDER,aberrant)
importFrom(OUTRIDER,filterExpression)
importFrom(OUTRIDER,plotAberrantPerSample)
importFrom(OUTRIDER,plotCountCorHeatmap)
importFrom(OUTRIDER,plotEncDimSearch)
importFrom(OUTRIDER,plotQQ)
importFrom(OUTRIDER,plotVolcano)
importFrom(OUTRIDER,results)
importFrom(PRROC,pr.curve)
importFrom(R.utils,renameFile)
importFrom(R.utils,withTimeout)
importFrom(RColorBrewer,brewer.pal)
importFrom(Rsamtools,"bamWhich<-")
importFrom(Rsamtools,BamFile)
importFrom(Rsamtools,ScanBamParam)
importFrom(Rsamtools,bamMapqFilter)
importFrom(Rsamtools,bamWhich)
importFrom(Rsamtools,idxstatsBam)
importFrom(Rsamtools,scanBamHeader)
importFrom(Rsubread,featureCounts)
importFrom(S4Vectors,"mcols<-")
importFrom(S4Vectors,"metadata<-")
importFrom(S4Vectors,"values<-")
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,Rle)
importFrom(S4Vectors,SimpleList)
importFrom(S4Vectors,elementMetadata)
importFrom(S4Vectors,end)
importFrom(S4Vectors,mcols)
importFrom(S4Vectors,metadata)
importFrom(S4Vectors,queryHits)
importFrom(S4Vectors,start)
importFrom(S4Vectors,subjectHits)
importFrom(S4Vectors,values)
importFrom(SummarizedExperiment,"assay<-")
importFrom(SummarizedExperiment,"assays<-")
importFrom(SummarizedExperiment,"colData<-")
importFrom(SummarizedExperiment,"rowRanges<-")
importFrom(SummarizedExperiment,Assays)
importFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,assayNames)
importFrom(SummarizedExperiment,assays)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rbind)
importFrom(SummarizedExperiment,rowData)
importFrom(SummarizedExperiment,rowRanges)
importFrom(VGAM,Coef)
importFrom(VGAM,betabinomial)
importFrom(VGAM,dbetabinom)
importFrom(VGAM,dbetabinom.ab)
importFrom(VGAM,pbetabinom)
importFrom(VGAM,pbetabinom.ab)
importFrom(VGAM,rbetabinom)
importFrom(VGAM,vglm)
importFrom(biomaRt,getBM)
importFrom(biomaRt,useEnsembl)
importFrom(cowplot,background_grid)
importFrom(cowplot,theme_cowplot)
importFrom(extraDistr,dbbinom)
importFrom(extraDistr,pbbinom)
importFrom(extraDistr,rdirmnom)
importFrom(generics,fit)
importFrom(ggplot2,aes)
importFrom(ggplot2,annotate)
importFrom(ggplot2,annotation_logticks)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,facet_grid)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_abline)
importFrom(ggplot2,geom_histogram)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_ribbon)
importFrom(ggplot2,geom_segment)
importFrom(ggplot2,geom_smooth)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,geom_vline)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,guide_legend)
importFrom(ggplot2,guides)
importFrom(ggplot2,labs)
importFrom(ggplot2,quo_name)
importFrom(ggplot2,scale_color_brewer)
importFrom(ggplot2,scale_color_discrete)
importFrom(ggplot2,scale_color_gradientn)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_colour_manual)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_linetype_manual)
importFrom(ggplot2,scale_x_log10)
importFrom(ggplot2,scale_y_log10)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggplot2,xlab)
importFrom(ggplot2,xlim)
importFrom(ggplot2,ylab)
importFrom(ggplot2,ylim)
importFrom(ggrepel,geom_text_repel)
importFrom(grDevices,colorRampPalette)
importFrom(matrixStats,colAnys)
importFrom(matrixStats,colMaxs)
importFrom(matrixStats,colMedians)
importFrom(matrixStats,colMins)
importFrom(methods,"slot<-")
importFrom(methods,as)
importFrom(methods,callNextMethod)
importFrom(methods,is)
importFrom(methods,new)
importFrom(methods,show)
importFrom(methods,slot)
importFrom(methods,validObject)
importFrom(pcaMethods,loadings)
importFrom(pcaMethods,pca)
importFrom(pheatmap,pheatmap)
importFrom(plotly,add_trace)
importFrom(plotly,ggplotly)
importFrom(plotly,layout)
importFrom(plotly,plot_ly)
importFrom(plotly,subplot)
importFrom(rhdf5,H5Dget_create_plist)
importFrom(rhdf5,H5Fclose)
importFrom(rhdf5,H5Fopen)
importFrom(rhdf5,H5Pclose)
importFrom(rhdf5,H5Pget_chunk)
importFrom(rhdf5,H5Pget_layout)
importFrom(rhdf5,h5delete)
importFrom(rhdf5,h5ls)
importFrom(stats,cor)
importFrom(stats,cutree)
importFrom(stats,dbinom)
importFrom(stats,dist)
importFrom(stats,hclust)
importFrom(stats,lm)
importFrom(stats,median)
importFrom(stats,na.omit)
importFrom(stats,optim)
importFrom(stats,optimize)
importFrom(stats,p.adjust)
importFrom(stats,pbinom)
importFrom(stats,pnorm)
importFrom(stats,ppoints)
importFrom(stats,predict)
importFrom(stats,qbeta)
importFrom(stats,quantile)
importFrom(stats,rbinom)
importFrom(stats,rlnorm)
importFrom(stats,rnbinom)
importFrom(stats,rnorm)
importFrom(stats,runif)
importFrom(stats,sd)
importFrom(tibble,"%>%")
importFrom(tibble,as_tibble)
importFrom(tools,file_path_as_absolute)
importFrom(txdbmaker,makeTxDbFromGFF)
importFrom(utils,capture.output)
importFrom(utils,packageVersion)
importFrom(utils,tail)
importMethodsFrom(OUTRIDER,results)
useDynLib(FRASER)
