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"' |