# Identify differential APA usage from RNA-seq alignments

## Documentation for package ‘roar’ version 1.20.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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"'