baySeq-classes          baySeq - classes
baySeq-package          Empirical Bayesian analysis of patterns of
                        differential expression in count data.
bimodalSep              A function that, given a numeric vector, finds
                        the value which splits the data into two sets
                        of minimal total variance.
factCount               Simulated data for testing the baySeq package
                        methods; simulated counts from a factorial
                        design differential expression analysis
factlibsizes            Simulated data for testing the baySeq package
                        methods; simulated library sizes from a
                        pairwise differential expression analysis
getLikelihoods          Finds posterior likelihoods for each count as
                        belonging to some hypothesis.
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
libsizes                Simulated data for testing the baySeq package
                        methods; simulated library sizes from a
                        pairwise differential expression analysis
plotMA.CD               'MA'-plot for count data.
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
simCount                Simulated data for testing the baySeq package
                        methods; simulated counts from a pairwise
                        differential expression analysis
simSeg                  Simulated data for testing the baySeq package
                        methods; simulated counts and segment lengths
                        from a pairwise differential expression
                        analysis
topCounts               Get the top counts corresponding to some group
                        from a 'countData' object
