RoarDataset             Creates a 'RoarDataset' object
RoarDataset-class       Class '"RoarDataset"'
RoarDatasetFromFiles    Creates a 'RoarDataset' object
RoarDatasetMultipleAPA
                        Creates a 'RoarDatasetMultipleAPA' object
RoarDatasetMultipleAPA-class
                        Class '"RoarDatasetMultipleAPA"'
RoarDatasetMultipleAPAFromFiles
                        Creates a 'RoarDatasetMultipleAPA' object
checkStep               Private/inner/helper method to check the order
                        of the invoked analysis methods
combineFisherMethod     Private/inner/helper method to combine pvalues
                        of independent test with the Fisher method
computePairedPvals      Computes pvalues (Fisher test) on the read
                        counts in this roar analysis
computePvals            Computes pvalues (Fisher test) on the read
                        counts in this roar analysis
computeRoars            Computes m/M and roar values
cores                   Method to check how many cores are used by a
                        roar analysis - right now not useful
countPrePost            Counts reads falling over PRE/POST portions of
                        the given transcripts
countResults            Returns a dataframe with results of the
                        analysis for a 'RoarDataset' object or a
                        'RoarDatasetMultipleAPA' object
fpkmResults             Returns a dataframe with results of the
                        analysis for a 'RoarDataset' object or a
                        'RoarDatasetMultipleAPA' object
getFisher               Private/inner/helper method to perform Fisher
                        test
meanAcrossAssays        Private/inner/helper method to get average
                        counts across samples
pvalueCorrectFilter     Returns a dataframe with results of the
                        analysis for a 'RoarDataset' object or a
                        'RoarDatasetMultipleAPA' object
pvalueFilter            Returns a dataframe with results of the
                        analysis for a 'RoarDataset' object or a
                        'RoarDatasetMultipleAPA' object
roar-package            Identify differential APA usage from RNA-seq
                        alignments
standardFilter          Returns a dataframe with results of the
                        analysis for a 'RoarDataset' object or a
                        'RoarDatasetMultipleAPA' object
totalResults            Returns a dataframe with results of the
                        analysis for a 'RoarDataset' or a
                        'RoarDatasetMultipleAPA' object
