# Find RAre Splicing Events in RNA-Seq Data

## Documentation for package ‘FRASER’ version 1.4.0

- 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
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