Find RAre Splicing Events in RNA-Seq Data

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Documentation for package ‘FRASER’ version 1.10.2

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

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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
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

-- B --

bamFile	Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. "
bamFile-method	Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. "
bamFile<-	Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. "
bamFile<--method	Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. "
bestQ	Getter/Setter functions

-- C --

calculatePadjValues	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 The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. "
condition-method	Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. "
condition<-	Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. "
condition<--method	Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. "
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 The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. "
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
fit	Fitting the denoising autoencoder
fit.FraserDataSet	Fitting the denoising autoencoder
FRASER	FRASER: Find RAre Splicing Events in RNA-seq data
FRASER.mcols.get	Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. "
FRASER.rowRanges.get	Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. "
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 The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. "
mergeCounts	Count RNA-seq data
mergeExternalData	Merge external data

-- N --

N	Getter/setter for count data
name	Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. "
name-method	Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. "
name<-	Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. "
name<--method	Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. "
nonSplicedReads	Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. "
nonSplicedReads-method	Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. "
nonSplicedReads<-	Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. "
nonSplicedReads<--method	Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. "

-- O --

optimHyperParams

Find optimal encoding dimension

-- P --

padjVals	Getter/Setter functions
padjVals,	Getter/Setter functions
pairedEnd	Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. "
pairedEnd-method	Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. "
pairedEnd<-	Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. "
pairedEnd<--method	Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. "
plotAberrantPerSample	Visualization functions for FRASER
plotAberrantPerSample-method	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
plotQQ	Visualization functions for FRASER
plotQQ-method	Visualization functions for FRASER
plotVolcano	Visualization functions for FRASER
plotVolcano-method	Visualization functions for FRASER
predictedMeans	Getter/Setter functions
pseudocount	Getter/Setter functions
psiTypes	Available psi types
pVals	Getter/Setter functions
pVals,	Getter/Setter functions

-- R --

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

-- S --

samples	Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. "
samples-method	Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. "
samples<-	Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. "
samples<--method	Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. "
saveFraserDataSet	Loading/Saving FraserDataSets
scanBamParam	Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. "
scanBamParam-method	Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. "
scanBamParam<-	Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. "
scanBamParam<--method	Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. "
strandSpecific	Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. "
strandSpecific-method	Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. "
strandSpecific<-	Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. "
strandSpecific<--method	Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. "
subset.FRASER	Subsetting by indices for junctions

-- V --

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

-- W --

workingDir	Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. "
workingDir-method	Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. "
workingDir<-	Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. "
workingDir<--method	Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. 'samples' sets or gets the sample IDs; 'condition' ; " 'nonSplicedReads' return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds. "

-- Z --

zScore,	Getter/Setter functions
zScores	Getter/Setter functions

-- misc --

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