CountDataSet-class      Class "CountDataSet" -- a container for count
                        data from HTS experiments
adjustScvForBias        Adjust an SCV value for the bias arising when
                        it is calculated from unbiased estimates of
                        mean and variance.
conditions              Accessor function for the conditions
                        information in a CountDataSet
counts                  Accessor for the 'counts' slot of a
                        CountDataSet object.
estimateSizeFactors     Estimate the size factors for a CountDataSet
estimateSizeFactorsForMatrix
                        Low-level function to estimate size factors
                        with robust regression.
estimateVarianceFunctionForMatrix
                        Lower-level function to estimate a raw variance
                        function.
estimateVarianceFunctions
                        Estimate the variance functions for a
                        CountDataSet.
getBaseMeansAndVariances
                        Perform row-wise estimates of base-level means
                        and variances for count data.
getVarianceStabilizedData
                        Perform a variance stabilising transformation
                        (VST) on the count data
makeExampleCountDataSet
                        make a simple example CountDataSet with random
                        data
nbinomTest              Test for differences between the base means for
                        two conditions
nbinomTestForMatrices   Perform row-wise tests for differences between
                        the base means of two count matrices.
newCountDataSet         Create a CountDataSet object
rawVarFunc              Accessor for raw variance functions
rawVarFuncTable         Accessor function for the slot rawVarFuncTable
                        of the class CountDataSet
residualsEcdfPlot       Produce a diagnostic plot to check the fit of a
                        raw variance function.
residualsEcdfPlotFromDiagnostics
                        Produce a diagnostic plot to check the fit of a
                        raw variance function.
scvPlot                 Produces a diagnostic plot with the variance
                        estimates, given as squared coefficients of
                        variation (SCV)
sizeFactors             Accessor functions for the sizeFactors
                        information in a CountDataSet
varianceFitDiagnostics
                        Generate a data frame with diagnostic
                        information on the fit of a base variance
                        function.
varianceFitDiagnosticsForMatrix
                        A lower-level function to get fit diagnostics
