aberrant,FraserDataSet-method	results
addCountsToFraserDataSet	countRNA
annotateIntronReferenceOverlap	potentialImpactAnnotations
annotatePotentialImpact	potentialImpactAnnotations
annotateRanges	annotateRanges
annotateRangesWithTxDb	annotateRanges
assayNames,FraserDataSet-method	assayNames-FraserDataSet-method
assays,FraserDataSet-method	assays-FraserDataSet-method
assays<-,FraserDataSet,DelayedMatrix-method	assays-FraserDataSet-method
assays<-,FraserDataSet,list-method	assays-FraserDataSet-method
assays<-,FraserDataSet,SimpleList-method	assays-FraserDataSet-method
availableFDRsubsets	getter_setter_functions
bamFile	fds-methods
bamFile,FraserDataSet-method	fds-methods
bamFile<-	fds-methods
bamFile<-,FraserDataSet-method	fds-methods
bestQ	getter_setter_functions
calculatePadjValues	FRASER
calculatePadjValuesOnSubset	FRASER
calculatePSIValues	calculatePSIValues
calculatePvalues	FRASER
calculateZscore	FRASER
condition	fds-methods
condition,FraserDataSet-method	fds-methods
condition<-	fds-methods
condition<-,FraserDataSet-method	fds-methods
countNonSplicedReads	countRNA
countRNA	countRNA
countRNAData	countRNA
counts,FraserDataSet-method	counts
counts<-,FraserDataSet,ANY-method	counts
countSplitReads	countRNA
createTestFraserDataSet	createTestFraserDataSet
createTestFraserSettings	createTestFraserDataSet
currentType	getter_setter_functions
currentType<-	getter_setter_functions
deltaPsiValue	getter_setter_functions
dontWriteHDF5	getter_setter_functions
dontWriteHDF5<-	getter_setter_functions
estimateBestQ	estimateBestQ
fds-methods	fds-methods
featureExclusionMask	getter_setter_functions
featureExclusionMask,	getter_setter_functions
featureExclusionMask<-	getter_setter_functions
filterExpression,FraserDataSet-method	filtering
filterExpressionAndVariability	filtering
filtering	filtering
filterVariability	filtering
filterVariability,FraserDataSet-method	filtering
fit	fit
fit.FraserDataSet	fit
fitMetrics	getter_setter_functions
fitMetrics<-	getter_setter_functions
flagBlacklistRegions	potentialImpactAnnotations
FRASER	FRASER
FRASER.mcols.get	fds-methods
FRASER.rowRanges.get	fds-methods
FraserDataSet	FraserDataSet
FraserDataSet-class	FraserDataSet-class
getNonSplitReadCountsForAllSamples	countRNA
getSplitReadCountsForAllSamples	countRNA
getter_setter_functions	getter_setter_functions
hyperParams	getter_setter_functions
injectOutliers	injectOutliers
K	counts
length,FraserDataSet-method	length-FraserDataSet-method
loadFraserDataSet	loadFraserDataSet
makeSimulatedFraserDataSet	makeSimulatedFraserDataSet
mapSeqlevels	fds-methods
mergeCounts	countRNA
mergeExternalData	mergeExternalData
N	counts
name	fds-methods
name,FraserDataSet-method	fds-methods
name<-	fds-methods
name<-,FraserDataSet-method	fds-methods
nonSplicedReads	fds-methods
nonSplicedReads,FraserDataSet-method	fds-methods
nonSplicedReads<-	fds-methods
nonSplicedReads<-,FraserDataSet-method	fds-methods
padjVals	getter_setter_functions
padjVals,	getter_setter_functions
pairedEnd	fds-methods
pairedEnd,FraserDataSet-method	fds-methods
pairedEnd<-	fds-methods
pairedEnd<-,FraserDataSet-method	fds-methods
plotAberrantPerSample	plotFunctions
plotAberrantPerSample,FraserDataSet-method	plotFunctions
plotBamCoverage	plotFunctions
plotBamCoverageFromResultTable	plotFunctions
plotCountCorHeatmap	plotFunctions
plotCountCorHeatmap,FraserDataSet-method	plotFunctions
plotEncDimSearch	plotFunctions
plotEncDimSearch,FraserDataSet-method	plotFunctions
plotExpectedVsObservedPsi	plotFunctions
plotExpression	plotFunctions
plotFilterExpression	plotFunctions
plotFilterVariability	plotFunctions
plotFunctions	plotFunctions
plotManhattan	plotFunctions
plotManhattan,FraserDataSet-method	plotFunctions
plotQQ	plotFunctions
plotQQ,FraserDataSet-method	plotFunctions
plotSpliceMetricRank	plotFunctions
plotVolcano	plotFunctions
plotVolcano,FraserDataSet-method	plotFunctions
potentialImpactAnnotations	potentialImpactAnnotations
predictedMeans	getter_setter_functions
pseudocount	getter_setter_functions
psiTypes	psiTypes
pVals	getter_setter_functions
pVals,	getter_setter_functions
results,FraserDataSet-method	results
rho	getter_setter_functions
rho,	getter_setter_functions
samples	fds-methods
samples,FraserDataSet-method	fds-methods
samples<-	fds-methods
samples<-,FraserDataSet-method	fds-methods
saveFraserDataSet	loadFraserDataSet
scanBamParam	fds-methods
scanBamParam,FraserDataSet-method	fds-methods
scanBamParam<-	fds-methods
scanBamParam<-,FraserDataSet-method	fds-methods
strandSpecific	fds-methods
strandSpecific,FraserDataSet-method	fds-methods
strandSpecific<-	fds-methods
strandSpecific<-,FraserDataSet-method	fds-methods
subset.FRASER	subset
verbose	getter_setter_functions
verbose<-	getter_setter_functions
workingDir	fds-methods
workingDir,FraserDataSet-method	fds-methods
workingDir<-	fds-methods
workingDir<-,FraserDataSet-method	fds-methods
zScore,	getter_setter_functions
zScores	getter_setter_functions
[,FraserDataSet,ANY,ANY,ANY-method	subset
`featureExclusionMask<-`	getter_setter_functions
