Advanced analysis using baySeq; generic distribution definitions

Analysis is carried out through specification of a densityFunction class. The primary value in a densityFunction object is the @density slot, a user-defined function that should take variables x, observables and parameters. x corresponds to a row of data in a countData object. observables is a list object of observed values that may influence the model. By default, the @libsizes and @seglens values of the countData object will be internally appended to this list, unless objects with these names are otherwise specified by the user. parameters is a list object of parameters to be empirically estimated from the data with the getPriors function and used to estimate likelihoods with the getLikelihoods function. The @dist function should return a vector of log-likelihood values (or NA for invalid parameter choices) of the same length as the input variable x.