data.A                  Sample data example for autosomal genes
data.X                  Sample data example for X chromosome genes
get.tausB               Produce _Xce_ estimates for mice with allele
                        specific reads
nLogLik                 Negative log likelihood for coefficients
                        provided in results of the fit using process
                        function
process                 Optimization wrapper, maximizing either the
                        joint model of total (TReC) and allele specific
                        (ASE) counts or just TReC
rcA                     Reformatted data for autosomal set to be used
                        as input to process function
rcX                     Reformatted data for chromosome X set to be
                        used as input to process function
readCounts              A list object that should be used as input to
                        optimization process function.
simRX                   Produce simulated counts
trecase.A.out           Example of results produced by optimizing step
                        using process function on autosomal genes.
                        Structured as a list.
trecase.X.out           Example of results produced by optimizing step
                        using process function on X chromosome genes.
                        Structured as a list.
