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"' |