allModels               Function to generate all possible models for a
                        countData object based on the replicate data.
baySeq-classes          baySeq - classes
baySeq-package          Empirical Bayesian analysis of patterns of
                        differential expression in count data.
bimodalSeparator        A function that, given a numeric vector, finds
                        the value which splits the data into two sets
                        of minimal total variance using Otsu's method.
CDPost                  'countData' object derived from data file
                        'simData' with estimated likelihoods of
                        differential expression.
CDPriors                'countData' object derived from data file
                        'simData' with estimated priors.
densityFunction-class   Class '"densityFunction"'
densityFunctions        Lists all currently available densityFunctions.
getLibsizes             Estimates library scaling factors (library
                        sizes) for count data.
getLikelihoods          Finds posterior likelihoods for each count or
                        paired count as belonging to some model.
getPosteriors           An internal function in the baySeq package for
                        calculating posterior likelihoods given
                        likelihoods of the data.
getPriors               Estimates prior parameters for the underlying
                        distributions of 'count' data.
getTPs                  Gets the number of true positives in the top n
                        counts selected by ranked posterior likelihoods
makeOrderings           Construct orderings for count data given a
                        model structure and an ordering function.
marginaliseEqual        Computes marginal likelihoods that two
                        replicate groups are equal.
marginalisePairwise     Computes marginal likelihoods that two
                        replicate groups differ, in a paticular
                        direction.
methObservables         Generation of intermediate values in likelihood
                        estimation for methylation data.
mobAnnotation           Annotation data for a set of small RNA loci
                        derived from sequencing of grafts of
                        Arabidopsis thaliana intended for differential
                        expression analyses.
mobData                 Data from a set of small RNA sequencing
                        experiments carried out on grafts of
                        Arabidopsis thaliana intended for differential
                        expression analyses.
pairData                Simulated data for testing the baySeq package
                        methods for paired data
plotMA.CD               'MA'-plot for count data.
plotNullPrior           Plots distribution of null function and shows
                        the threshold separator.
plotPosteriors          Plots the posterior likelihoods estimated for a
                        'countData' object against the log-ratios
                        observed between two sets of sample data.
plotPriors              Plots the density of the log values estimated
                        for the mean rate in the prior data for the
                        Negative Binomial approach to detecting
                        differential expression
selectTop               Selects the top genomic events, based on
                        posterior likelihoods, from a 'countData'
                        object.
simData                 Simulated data for testing the baySeq package
                        methods
summarisePosteriors     Summarises expected number of genomic events
                        given the calculated posterior likelihoods of a
                        countData object.
topCounts               Get the top counts corresponding to some group
                        from a 'countData' object
zimData                 Simulated data for testing the baySeq package
                        methods
