FRASER                  FRASER: Find RAre Splicing Events in RNA-seq
                        data
FraserDataSet           The FRASER dataset object
FraserDataSet-class     FraserDataSet
K                       Getter/setter for count data
annotateRanges          Annotates the given FraserDataSet with the HGNC
                        symbol with biomaRt
assayNames,FraserDataSet-method
                        Returns the assayNames of FRASER
assays,FraserDataSet-method
                        Returns the assay for the given name/index of
                        the FraserDataSet
calculatePSIValues      PSI value calculation
countRNA                Count RNA-seq data
createTestFraserSettings
                        Create a test dataset
filtering               Filtering FraserDataSets
fit                     Fitting the denoising autoencoder
getter_setter_functions
                        Getter/Setter functions
injectOutliers          Inject artificial outliers in an existing fds
length,FraserDataSet-method
                        retrieve the length of the object (aka number
                        of junctions)
loadFraserDataSet       Loading/Saving FraserDataSets
makeSimulatedFraserDataSet
                        Create an simulated example data set for FRASER
mergeExternalData       Merge external data
optimHyperParams        Find optimal encoding dimension
plotFunctions           Visualization functions for FRASER
psiTypes                Available psi types
results,FraserDataSet-method
                        Extracting results and aberrant splicing events
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. "
subset.FRASER           Subsetting by indices for junctions
