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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 |
| 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 |
| 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"' |