# 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%",
  chunk,
  is.error,
  isFALSE,
  isScalarCharacter,
  isScalarInteger,
  isScalarLogical,
  isScalarNumeric,
  isScalarValue,
  seq_col,
  seq_row
)
importFrom(BSgenome,getBSgenome)
importFrom(Biobase,rowMax)
importFrom(BiocGenerics,
  "counts<-",
  "strand<-",
  cbind,
  counts,
  strand,
  updateObject,
  which
)
importFrom(DelayedArray,
  "path<-",
  DelayedArray,
  plogis,
  qlogis,
  rowMaxs,
  rowMeans
)
importFrom(DelayedMatrixStats,
  colMeans2,
  colSds,
  rowMeans2,
  rowMedians,
  rowQuantiles,
  rowSds
)
importFrom(GenomeInfoDb,
  "seqlengths<-",
  "seqlevels<-",
  "seqlevelsStyle<-",
  dropSeqlevels,
  keepSeqlevels,
  keepStandardChromosomes,
  seqinfo,
  seqlengths,
  seqlevels,
  seqlevelsStyle,
  seqnames,
  sortSeqlevels,
  standardChromosomes
)
importFrom(GenomicAlignments,
  junctions,
  readGAlignmentPairs,
  readGAlignments,
  summarizeJunctions
)
importFrom(GenomicFeatures,
  exons,
  fiveUTRsByTranscript,
  genes,
  intronsByTranscript,
  seqlevels0,
  threeUTRsByTranscript
)
importFrom(GenomicRanges,
  "end<-",
  "seqinfo<-",
  "start<-",
  GRanges,
  GRangesList,
  end,
  findOverlaps,
  granges,
  invertStrand,
  makeGRangesFromDataFrame,
  start
)
importFrom(HDF5Array,
  HDF5Array,
  loadHDF5SummarizedExperiment,
  path,
  saveHDF5SummarizedExperiment,
  writeHDF5Array
)
importFrom(IRanges,
  "%over%",
  IRanges,
  distance,
  from,
  nearest,
  ranges,
  subsetByOverlaps,
  to
)
importFrom(OUTRIDER,
  aberrant,
  filterExpression,
  plotAberrantPerSample,
  plotCountCorHeatmap,
  plotEncDimSearch,
  plotQQ,
  plotVolcano,
  results
)
importFrom(PRROC,pr.curve)
importFrom(R.utils,
  renameFile,
  withTimeout
)
importFrom(RColorBrewer,brewer.pal)
importFrom(Rsamtools,
  "bamWhich<-",
  BamFile,
  ScanBamParam,
  bamMapqFilter,
  bamWhich,
  idxstatsBam,
  scanBamHeader
)
importFrom(Rsubread,featureCounts)
importFrom(S4Vectors,
  "mcols<-",
  "metadata<-",
  "values<-",
  DataFrame,
  Rle,
  SimpleList,
  elementMetadata,
  end,
  mcols,
  metadata,
  queryHits,
  start,
  subjectHits,
  values
)
importFrom(SummarizedExperiment,
  "assay<-",
  "assays<-",
  "colData<-",
  "rowRanges<-",
  Assays,
  SummarizedExperiment,
  assay,
  assayNames,
  assays,
  colData,
  rbind,
  rowData,
  rowRanges
)
importFrom(VGAM,
  Coef,
  betabinomial,
  dbetabinom,
  dbetabinom.ab,
  pbetabinom,
  pbetabinom.ab,
  rbetabinom,
  vglm
)
importFrom(biomaRt,
  getBM,
  useEnsembl
)
importFrom(cowplot,
  background_grid,
  theme_cowplot
)
importFrom(extraDistr,
  dbbinom,
  pbbinom,
  rdirmnom
)
importFrom(generics,fit)
importFrom(ggplot2,
  aes,
  annotate,
  annotation_logticks,
  element_blank,
  facet_grid,
  facet_wrap,
  geom_abline,
  geom_histogram,
  geom_hline,
  geom_line,
  geom_point,
  geom_ribbon,
  geom_segment,
  geom_smooth,
  geom_text,
  geom_vline,
  ggplot,
  ggtitle,
  guide_legend,
  guides,
  labs,
  quo_name,
  scale_color_brewer,
  scale_color_discrete,
  scale_color_gradientn,
  scale_color_manual,
  scale_colour_manual,
  scale_fill_manual,
  scale_linetype_manual,
  scale_x_log10,
  scale_y_log10,
  theme,
  theme_bw,
  xlab,
  xlim,
  ylab,
  ylim
)
importFrom(ggrepel,geom_text_repel)
importFrom(grDevices,colorRampPalette)
importFrom(matrixStats,
  colAnys,
  colMaxs,
  colMedians,
  colMins
)
importFrom(methods,
  "slot<-",
  as,
  callNextMethod,
  is,
  new,
  show,
  slot,
  validObject
)
importFrom(pcaMethods,
  loadings,
  pca
)
importFrom(pheatmap,pheatmap)
importFrom(plotly,
  add_trace,
  ggplotly,
  layout,
  plot_ly,
  subplot
)
importFrom(rhdf5,
  H5Dget_create_plist,
  H5Fclose,
  H5Fopen,
  H5Pclose,
  H5Pget_chunk,
  H5Pget_layout,
  h5delete,
  h5ls
)
importFrom(stats,
  cor,
  cutree,
  dbinom,
  dist,
  hclust,
  lm,
  median,
  na.omit,
  optim,
  optimize,
  p.adjust,
  pbinom,
  pnorm,
  ppoints,
  predict,
  qbeta,
  quantile,
  rbinom,
  rlnorm,
  rnbinom,
  rnorm,
  runif,
  sd
)
importFrom(tibble,
  "%>%",
  as_tibble
)
importFrom(tools,file_path_as_absolute)
importFrom(txdbmaker,makeTxDbFromGFF)
importFrom(utils,
  capture.output,
  packageVersion,
  tail
)
importMethodsFrom(OUTRIDER,results)
useDynLib(FRASER)
