Combined Total and Allele Specific Reads Sequencing Study

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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.