| 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. |