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
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
getRawScvDistanceMatrix
                        Calculates a matrix of "distances" between
                        samples
getRawScvForSamplePair
                        for a pair of samples, calculate the average
                        raw SCV between them, as a
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
nbkd.sf                 GLM family for a negative binomial with known
                        dispersion and log link
newCountDataSet         Create a CountDataSet object
rawVarFunc              Accessor for raw variance functions
rawVarFuncTable         Accessor functions for the slot rawVarFuncTable
                        of the class
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
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
varianceFitDiagnosticsForMatrix
                        A lower-level function to get fit diagnostics
