Identify differential APA usage from RNA-seq alignments


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Documentation for package ‘roar’ version 1.6.1

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roar-package Identify differential APA usage from RNA-seq alignments
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) for this 'RoarDataset' object
computePairedPvals-method Class '"RoarDataset"'
computePvals Computes pvalues (Fisher test) for this 'RoarDataset' object
computePvals-method Class '"RoarDataset"'
computeRoars Computes m/M and roar values for this 'RoarDataset' object
computeRoars-method Class '"RoarDataset"'
cores Method to check how many cores are used by a roar analysis - right now not useful
cores-method Class '"RoarDataset"'
countPrePost Counts reads falling over PRE/POST portions of the given transcripts
countPrePost-method Class '"RoarDataset"'
countResults Returns a dataframe with results of the analysis for a 'RoarDataset' object
countResults-method Class '"RoarDataset"'
fpkmResults Returns a dataframe with results of the analysis for a 'RoarDataset' object
fpkmResults-method Class '"RoarDataset"'
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
pvalueCorrectFilter-method Class '"RoarDataset"'
pvalueFilter Returns a dataframe with results of the analysis for a 'RoarDataset' object
pvalueFilter-method Class '"RoarDataset"'
roar Identify differential APA usage from RNA-seq alignments
RoarDataset Creates a 'RoarDataset' object
RoarDataset-class Class '"RoarDataset"'
RoarDatasetFromFiles Creates a 'RoarDataset' object
standardFilter Returns a dataframe with results of the analysis for a 'RoarDataset' object
standardFilter-method Class '"RoarDataset"'
totalResults Returns a dataframe with results of the analysis for a 'RoarDataset' object
totalResults-method Class '"RoarDataset"'