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.

Author
Vasyl Zhabotynsky [aut, cre], Wei Sun [aut], Fei Zou [aut]
Date of publication
2016-12-01 12:45:14
Maintainer
Vasyl Zhabotynsky <vasyl@unc.edu>
License
GPL (>= 2)
Version
0.99.3

View on CRAN

Man 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...
process
Optimization wrapper, maximizing either the joint model of...
rcA
Reformatted data for autosomal set to be used as input to...
rcX
Reformatted data for chromosome X set to be used as input to...
readCounts
A list object that should be used as input to optimization...
simRX
Produce simulated counts
trecase.A.out
Example of results produced by optimizing step using process...
trecase.X.out
Example of results produced by optimizing step using process...

Files in this package

rxSeq
rxSeq/inst
rxSeq/inst/doc
rxSeq/inst/doc/rxSeq.pdf
rxSeq/inst/doc/rxSeq.Rnw
rxSeq/inst/doc/rxSeq.R
rxSeq/NAMESPACE
rxSeq/data
rxSeq/data/dt.X.rda
rxSeq/data/dt.A.rda
rxSeq/R
rxSeq/R/get.better.R
rxSeq/R/nLogLik.trecase.A.R
rxSeq/R/ll.toRCI.X.R
rxSeq/R/trecase.sex.X.R
rxSeq/R/ll.toRCI.b0.A1.R
rxSeq/R/trecase.full.A.R
rxSeq/R/ll.jRCI.sex.X.R
rxSeq/R/ll.toRCI.b0.X.R
rxSeq/R/ll.aRC.theta.A1.R
rxSeq/R/ll.jRCI.A.cons1.R
rxSeq/R/trec.dev.X.R
rxSeq/R/ll.jRCI.A.R
rxSeq/R/trec.dom.A.R
rxSeq/R/ll.jRCI.b0.A.R
rxSeq/R/ll.toRCI.sex.A.R
rxSeq/R/input.checks.X.R
rxSeq/R/ll.jRCI.trec.ase.X.R
rxSeq/R/proc.trecase.X.R
rxSeq/R/ll.aRC.R
rxSeq/R/logBB.R
rxSeq/R/nLogLik.trecase.X.R
rxSeq/R/ll.jRCI.b1.A2.R
rxSeq/R/ll.toRCI.sex.b0.A.R
rxSeq/R/trecase.dom.A.R
rxSeq/R/trec.b1.A.R
rxSeq/R/trec.sex.dom.A.R
rxSeq/R/ll.jRCI.sex.b1.A.R
rxSeq/R/ll.jRCI.sex.b0.X.R
rxSeq/R/ll.jRCI.A1.R
rxSeq/R/ll.jRCI.ase.b0.X.R
rxSeq/R/proc.trec.A.R
rxSeq/R/ll.tRCI.iphi.A.R
rxSeq/R/trec.sex.A.R
rxSeq/R/readCounts.R
rxSeq/R/ll.jRCI.ase.b0.A.R
rxSeq/R/trec.sex.b1.A.R
rxSeq/R/ll.jRCI.ase.b0.A1.R
rxSeq/R/trec.sex.b0.A.R
rxSeq/R/nLogLik.trec.A.R
rxSeq/R/ll.toRCI.iphi.A.R
rxSeq/R/trecase.b0.A.R
rxSeq/R/get.tausB.R
rxSeq/R/trecase.ase.b0.X.R
rxSeq/R/loglikNB0.R
rxSeq/R/trecase.sex.A.R
rxSeq/R/ll.jRCI.A.cons.R
rxSeq/R/trec.sex.X.R
rxSeq/R/ll.jRCI.b1.A1.R
rxSeq/R/ll.toRCI.sex.X.R
rxSeq/R/loglikNB2.R
rxSeq/R/ll.tRCI.iphi.X.R
rxSeq/R/trecase.full.A.cons.R
rxSeq/R/ll.aRC.X.R
rxSeq/R/trecase.b1.X.R
rxSeq/R/ll.jRCI.trec.ase.A1.R
rxSeq/R/trecase.b0.X.R
rxSeq/R/ll.toRCI.iphi.X.R
rxSeq/R/test.R
rxSeq/R/loglikNB.R
rxSeq/R/ll.jRCI.sex.b0.A.R
rxSeq/R/simRX.R
rxSeq/R/ll.jRCI.sex.A.R
rxSeq/R/trecase.trec.ase.A.R
rxSeq/R/ll.jRCI.b1.X.R
rxSeq/R/trecase.dom.X.R
rxSeq/R/trecase.sex.b0.X.R
rxSeq/R/ll.toRCI.A.R
rxSeq/R/trecase.trec.ase.X.R
rxSeq/R/process.R
rxSeq/R/ll.tRCI.A.R
rxSeq/R/trecase.b1.A.R
rxSeq/R/ll.jRCI.b0.X.R
rxSeq/R/trec.full.A.R
rxSeq/R/trec.b0.A.R
rxSeq/R/ll.jRCI.ase.b0.A2.R
rxSeq/R/ll.jRCI.b0.A2.R
rxSeq/R/ll.jRCI.b1.A.R
rxSeq/R/ll.aRC.theta.A.R
rxSeq/R/trecase.ase.b0.A.R
rxSeq/R/loglikNB1.R
rxSeq/R/trec.full.X.R
rxSeq/R/ll.toRCI.b0.A.R
rxSeq/R/nLogLik.trec.X.R
rxSeq/R/trecase.full.X.R
rxSeq/R/trec.b1.X.R
rxSeq/R/get.tauB.R
rxSeq/R/get.inits.R
rxSeq/R/trecase.sex.dom.A.R
rxSeq/R/trec.sex.b0.X.R
rxSeq/R/ll.tRCI.X.R
rxSeq/R/ll.aRC.theta.A2.R
rxSeq/R/proc.trecase.A.R
rxSeq/R/proc.trec.X.R
rxSeq/R/ll.jRCI.X.R
rxSeq/R/nLogLik.R
rxSeq/R/ll.jRCI.A2.R
rxSeq/R/ll.toRCI.b0.A2.R
rxSeq/R/trec.dom.X.R
rxSeq/R/ll.jRCI.trec.ase.A.R
rxSeq/R/ll.jRCI.A.cons2.R
rxSeq/R/ll.jRCI.b0.A1.R
rxSeq/R/input.checks.A.R
rxSeq/R/trecase.dev.X.R
rxSeq/R/ll.aRC.theta.X.R
rxSeq/R/trecase.sex.b0.A.R
rxSeq/R/ll.jRCI.trec.ase.A2.R
rxSeq/R/trec.b0.X.R
rxSeq/R/trecase.sex.b1.A.R
rxSeq/R/ll.toRCI.sex.b0.X.R
rxSeq/vignettes
rxSeq/vignettes/rxSeq.Rnw
rxSeq/MD5
rxSeq/build
rxSeq/build/vignette.rds
rxSeq/DESCRIPTION
rxSeq/man
rxSeq/man/rcX.Rd
rxSeq/man/rcA.Rd
rxSeq/man/trecase.X.out.Rd
rxSeq/man/trecase.A.out.Rd
rxSeq/man/nLogLik.Rd
rxSeq/man/data.X.Rd
rxSeq/man/readCounts.Rd
rxSeq/man/simRX.Rd
rxSeq/man/data.A.Rd
rxSeq/man/get.tausB.Rd
rxSeq/man/process.Rd