Identify differential APA usage from RNA-seq alignments

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Documentation for package ‘roar’ version 1.44.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
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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) on the read counts in this roar analysis
computePairedPvals, RoarDataset	Computes pvalues (Fisher test) on the read counts in this roar analysis
computePairedPvals, RoarDatasetMultipleAPA	Computes pvalues (Fisher test) on the read counts in this roar analysis
computePairedPvals-method	Class '"RoarDataset"'
computePairedPvals-method	Class '"RoarDatasetMultipleAPA"'
computePvals	Computes pvalues (Fisher test) on the read counts in this roar analysis
computePvals, RoarDataset	Computes pvalues (Fisher test) on the read counts in this roar analysis
computePvals, RoarDatasetMultipleAPA	Computes pvalues (Fisher test) on the read counts in this roar analysis
computePvals-method	Class '"RoarDataset"'
computePvals-method	Class '"RoarDatasetMultipleAPA"'
computeRoars	Computes m/M and roar values
computeRoars, RoarDataset, numeric, numeric	Computes m/M and roar values
computeRoars, RoarDatasetMultipleAPA, numeric, numeric	Computes m/M and roar values
computeRoars-method	Class '"RoarDataset"'
computeRoars-method	Class '"RoarDatasetMultipleAPA"'
cores	Method to check how many cores are used by a roar analysis - right now not useful
cores-method	Class '"RoarDataset"'
cores-method	Class '"RoarDatasetMultipleAPA"'
countPrePost	Counts reads falling over PRE/POST portions of the given transcripts
countPrePost,RoarDataset,logical	Counts reads falling over PRE/POST portions of the given transcripts
countPrePost,RoarDatasetMultipleAPA	Counts reads falling over PRE/POST portions of the given transcripts
countPrePost-method	Class '"RoarDataset"'
countPrePost-method	Class '"RoarDatasetMultipleAPA"'
countResults	Returns a dataframe with results of the analysis for a 'RoarDataset' object or a 'RoarDatasetMultipleAPA' object
countResults, RoarDataset	Returns a dataframe with results of the analysis for a 'RoarDataset' object or a 'RoarDatasetMultipleAPA' object
countResults, RoarDatasetMultipleAPA	Returns a dataframe with results of the analysis for a 'RoarDataset' object or a 'RoarDatasetMultipleAPA' object
countResults-method	Class '"RoarDataset"'
countResults-method	Class '"RoarDatasetMultipleAPA"'
fpkmResults	Returns a dataframe with results of the analysis for a 'RoarDataset' object or a 'RoarDatasetMultipleAPA' object
fpkmResults, RoarDataset	Returns a dataframe with results of the analysis for a 'RoarDataset' object or a 'RoarDatasetMultipleAPA' object
fpkmResults, RoarDatasetMultipleAPA	Returns a dataframe with results of the analysis for a 'RoarDataset' object or a 'RoarDatasetMultipleAPA' object
fpkmResults-method	Class '"RoarDataset"'
fpkmResults-method	Class '"RoarDatasetMultipleAPA"'
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
pvalueCorrectFilter, RoarDataset	Returns a dataframe with results of the analysis for a 'RoarDataset' object or a 'RoarDatasetMultipleAPA' object
pvalueCorrectFilter, RoarDatasetMultipleAPA	Returns a dataframe with results of the analysis for a 'RoarDataset' object or a 'RoarDatasetMultipleAPA' object
pvalueCorrectFilter-method	Class '"RoarDataset"'
pvalueCorrectFilter-method	Class '"RoarDatasetMultipleAPA"'
pvalueFilter	Returns a dataframe with results of the analysis for a 'RoarDataset' object or a 'RoarDatasetMultipleAPA' object
pvalueFilter, RoarDataset	Returns a dataframe with results of the analysis for a 'RoarDataset' object or a 'RoarDatasetMultipleAPA' object
pvalueFilter, RoarDatasetMultipleAPA	Returns a dataframe with results of the analysis for a 'RoarDataset' object or a 'RoarDatasetMultipleAPA' object
pvalueFilter-method	Class '"RoarDataset"'
pvalueFilter-method	Class '"RoarDatasetMultipleAPA"'
roar	Identify differential APA usage from RNA-seq alignments
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
standardFilter	Returns a dataframe with results of the analysis for a 'RoarDataset' object or a 'RoarDatasetMultipleAPA' object
standardFilter, RoarDataset	Returns a dataframe with results of the analysis for a 'RoarDataset' object or a 'RoarDatasetMultipleAPA' object
standardFilter, RoarDatasetMultipleAPA	Returns a dataframe with results of the analysis for a 'RoarDataset' object or a 'RoarDatasetMultipleAPA' object
standardFilter-method	Class '"RoarDataset"'
standardFilter-method	Class '"RoarDatasetMultipleAPA"'
totalResults	Returns a dataframe with results of the analysis for a 'RoarDataset' or a 'RoarDatasetMultipleAPA' object
totalResults, RoarDataset	Returns a dataframe with results of the analysis for a 'RoarDataset' or a 'RoarDatasetMultipleAPA' object
totalResults, RoarDatasetMultipleAPA	Returns a dataframe with results of the analysis for a 'RoarDataset' or a 'RoarDatasetMultipleAPA' object
totalResults-method	Class '"RoarDataset"'
totalResults-method	Class '"RoarDatasetMultipleAPA"'