R: Combined Total and Allele Specific Reads Sequencing Study

# Combined Total and Allele Specific Reads Sequencing Study

## Documentation for package ‘rxSeq’ version 0.99.3

- DESCRIPTION file
- User guides, package vignettes and other documentation

## Help Pages

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.