Package: rxSeq 0.99.3

Vasyl Zhabotynsky

rxSeq: Combined Total and Allele Specific Reads Sequencing Study

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

Authors:Vasyl Zhabotynsky [aut, cre], Wei Sun [aut], Fei Zou [aut]

# Install 'rxSeq' in R:

install.packages('rxSeq', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

data.A - Sample data example for autosomal genes
data.X - Sample data example for X chromosome genes
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
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.

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

Last updated from:d46a886029. Checks:6 OK. Indexed: yes.

Target	Result	Time
linux-devel	OK	123
source / vignettes	OK	183
linux-release	OK	129
windows-devel	OK	80
windows-release	OK	88
wasm-release	OK	98

Dependencies:MASS numDeriv VGAM

Last update: 2016-12-01
Started: 2016-12-01

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