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 functions 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.
getRawScvDistanceMatrix
                        Calculates a matrix of "distances" between
                        samples
getRawScvForSamplePair
                        for a pair of samples, calculate the average
                        raw SCV between them, as a measure of noise
getVarianceStabilizedData
                        Perform a variance stabilising transformation
                        (VST) on the count data
makeExampleCountDataSet
                        make a simple example CountDataSet with random
                        data
nbinomFitGLM            Fit a generalized linear model (GLM) for each
                        gene.
nbinomGLMTest           Perform chi-squared tests comparing two sets of
                        GLM fits
nbinomGLMsForMatrix     Fit negative binomial GLMs to a count matrix.
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.
nbkd.sf                 GLM family for a negative binomial with known
                        dispersion and log link with size factors
newCountDataSet         Create a CountDataSet object
rawVarFunc              Accessor for raw variance functions
rawVarFuncTable         Accessor functions 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
varAdjFactors           Defunct function. Do not use.
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
