Identify differential APA usage from RNA-seq alignments


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Documentation for package ‘roar’ version 1.10.0

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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"'