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rxSeq (version 0.99.3)

Combined Total and Allele Specific Reads Sequencing Study

Description

Analysis of combined total and allele specific reads from the reciprocal cross study with RNA-seq data.

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Version

Install

install.packages('rxSeq')

Monthly Downloads

128

Version

0.99.3

License

GPL (>= 2)

Maintainer

Vasyl Zhabotynsky

Last Published

December 1st, 2016

Functions in rxSeq (0.99.3)

data.X

Sample data example for X chromosome genes
data.A

Sample data example for autosomal genes
process

Optimization wrapper, maximizing either the joint model of total (TReC) and allele specific (ASE) counts or just TReC
trecase.X.out

Example of results produced by optimizing step using process function on X chromosome genes. Structured as a list.
rcA

Reformatted data for autosomal set to be used as input to process function
trecase.A.out

Example of results produced by optimizing step using process function on autosomal genes. Structured as a list.
rcX

Reformatted data for chromosome X set to be used as input to process function
simRX

Produce simulated counts
readCounts

A list object that should be used as input to optimization process function.
nLogLik

Negative log likelihood for coefficients provided in results of the fit using process function
get.tausB

Produce Xce estimates for mice with allele specific reads