Find RAre Splicing Events in RNA-Seq Data

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Documentation for package ‘FRASER’ version 2.3.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

A B C D F G H I K L M N O P R S V W Z misc

-- A --

aberrant-method	Extracting results and aberrant splicing events
addCountsToFraserDataSet	Count RNA-seq data
annotateIntronReferenceOverlap	Additional result annotations
annotatePotentialImpact	Additional result annotations
annotateRanges	Annotates the given FraserDataSet with the HGNC symbol with biomaRt
annotateRangesWithTxDb	Annotates the given FraserDataSet with the HGNC symbol with biomaRt
assayNames-method	Returns the assayNames of FRASER
assays-method	Returns the assay for the given name/index of the FraserDataSet
assays<--method	Returns the assay for the given name/index of the FraserDataSet
availableFDRsubsets	Getter/Setter functions

-- B --

bamFile	Getter/Setter methods for the FraserDataSet
bamFile-method	Getter/Setter methods for the FraserDataSet
bamFile<-	Getter/Setter methods for the FraserDataSet
bamFile<--method	Getter/Setter methods for the FraserDataSet
bestQ	Getter/Setter functions

-- C --

calculatePadjValues	FRASER: Find RAre Splicing Events in RNA-seq data
calculatePadjValuesOnSubset	FRASER: Find RAre Splicing Events in RNA-seq data
calculatePSIValues	PSI value calculation
calculatePvalues	FRASER: Find RAre Splicing Events in RNA-seq data
calculateZscore	FRASER: Find RAre Splicing Events in RNA-seq data
condition	Getter/Setter methods for the FraserDataSet
condition-method	Getter/Setter methods for the FraserDataSet
condition<-	Getter/Setter methods for the FraserDataSet
condition<--method	Getter/Setter methods for the FraserDataSet
countNonSplicedReads	Count RNA-seq data
countRNA	Count RNA-seq data
countRNAData	Count RNA-seq data
counts-method	Getter/setter for count data
counts<--method	Getter/setter for count data
countSplitReads	Count RNA-seq data
createTestFraserDataSet	Create a test dataset
createTestFraserSettings	Create a test dataset
currentType	Getter/Setter functions
currentType<-	Getter/Setter functions

-- D --

deltaPsiValue	Getter/Setter functions
dontWriteHDF5	Getter/Setter functions
dontWriteHDF5<-	Getter/Setter functions

-- F --

fds-methods	Getter/Setter methods for the FraserDataSet
featureExclusionMask	Getter/Setter functions
featureExclusionMask,	Getter/Setter functions
featureExclusionMask<-	Getter/Setter functions
filterExpression-method	Filtering FraserDataSets
filterExpressionAndVariability	Filtering FraserDataSets
filtering	Filtering FraserDataSets
filterVariability	Filtering FraserDataSets
filterVariability-method	Filtering FraserDataSets
fit	Fitting the denoising autoencoder
fit.FraserDataSet	Fitting the denoising autoencoder
fitMetrics	Getter/Setter functions
fitMetrics<-	Getter/Setter functions
flagBlacklistRegions	Additional result annotations
FRASER	FRASER: Find RAre Splicing Events in RNA-seq data
FRASER.mcols.get	Getter/Setter methods for the FraserDataSet
FRASER.rowRanges.get	Getter/Setter methods for the FraserDataSet
FraserDataSet	The FRASER dataset object
FraserDataSet-class	FraserDataSet

-- G --

getNonSplitReadCountsForAllSamples	Count RNA-seq data
getSplitReadCountsForAllSamples	Count RNA-seq data
getter_setter_functions	Getter/Setter functions

-- H --

hyperParams

Getter/Setter functions

-- I --

injectOutliers

Inject artificial outliers in an existing fds

-- K --

K	Getter/setter for count data

-- L --

length-method	retrieve the length of the object (aka number of junctions)
loadFraserDataSet	Loading/Saving FraserDataSets

-- M --

makeSimulatedFraserDataSet	Create an simulated example data set for FRASER
mapSeqlevels	Getter/Setter methods for the FraserDataSet
mergeCounts	Count RNA-seq data
mergeExternalData	Merge external data

-- N --

N	Getter/setter for count data
name	Getter/Setter methods for the FraserDataSet
name-method	Getter/Setter methods for the FraserDataSet
name<-	Getter/Setter methods for the FraserDataSet
name<--method	Getter/Setter methods for the FraserDataSet
nonSplicedReads	Getter/Setter methods for the FraserDataSet
nonSplicedReads-method	Getter/Setter methods for the FraserDataSet
nonSplicedReads<-	Getter/Setter methods for the FraserDataSet
nonSplicedReads<--method	Getter/Setter methods for the FraserDataSet

-- O --

optimHyperParams

Find optimal encoding dimension

-- P --

padjVals	Getter/Setter functions
padjVals,	Getter/Setter functions
pairedEnd	Getter/Setter methods for the FraserDataSet
pairedEnd-method	Getter/Setter methods for the FraserDataSet
pairedEnd<-	Getter/Setter methods for the FraserDataSet
pairedEnd<--method	Getter/Setter methods for the FraserDataSet
plotAberrantPerSample	Visualization functions for FRASER
plotAberrantPerSample-method	Visualization functions for FRASER
plotBamCoverage	Visualization functions for FRASER
plotBamCoverageFromResultTable	Visualization functions for FRASER
plotCountCorHeatmap	Visualization functions for FRASER
plotCountCorHeatmap-method	Visualization functions for FRASER
plotEncDimSearch	Visualization functions for FRASER
plotEncDimSearch-method	Visualization functions for FRASER
plotExpectedVsObservedPsi	Visualization functions for FRASER
plotExpression	Visualization functions for FRASER
plotFilterExpression	Visualization functions for FRASER
plotFilterVariability	Visualization functions for FRASER
plotFunctions	Visualization functions for FRASER
plotManhattan	Visualization functions for FRASER
plotManhattan-method	Visualization functions for FRASER
plotQQ	Visualization functions for FRASER
plotQQ-method	Visualization functions for FRASER
plotSpliceMetricRank	Visualization functions for FRASER
plotVolcano	Visualization functions for FRASER
plotVolcano-method	Visualization functions for FRASER
potentialImpactAnnotations	Additional result annotations
predictedMeans	Getter/Setter functions
pseudocount	Getter/Setter functions
psiTypes	Available splice metrics
pVals	Getter/Setter functions
pVals,	Getter/Setter functions

-- R --

results-method	Extracting results and aberrant splicing events
rho	Getter/Setter functions
rho,	Getter/Setter functions

-- S --

samples	Getter/Setter methods for the FraserDataSet
samples-method	Getter/Setter methods for the FraserDataSet
samples<-	Getter/Setter methods for the FraserDataSet
samples<--method	Getter/Setter methods for the FraserDataSet
saveFraserDataSet	Loading/Saving FraserDataSets
scanBamParam	Getter/Setter methods for the FraserDataSet
scanBamParam-method	Getter/Setter methods for the FraserDataSet
scanBamParam<-	Getter/Setter methods for the FraserDataSet
scanBamParam<--method	Getter/Setter methods for the FraserDataSet
strandSpecific	Getter/Setter methods for the FraserDataSet
strandSpecific-method	Getter/Setter methods for the FraserDataSet
strandSpecific<-	Getter/Setter methods for the FraserDataSet
strandSpecific<--method	Getter/Setter methods for the FraserDataSet
subset.FRASER	Subsetting by indices for junctions

-- V --

verbose	Getter/Setter functions
verbose<-	Getter/Setter functions

-- W --

workingDir	Getter/Setter methods for the FraserDataSet
workingDir-method	Getter/Setter methods for the FraserDataSet
workingDir<-	Getter/Setter methods for the FraserDataSet
workingDir<--method	Getter/Setter methods for the FraserDataSet

-- Z --

zScore,	Getter/Setter functions
zScores	Getter/Setter functions

-- misc --

[-method	Subsetting by indices for junctions
`featureExclusionMask<-`	Getter/Setter functions