cubfits: Codon Usage Bias Fits

Estimating mutation and selection coefficients on synonymous codon bias usage based on models of ribosome overhead cost (ROC). Multinomial logistic regression and Markov Chain Monte Carlo are used to estimate and predict protein production rates with/without the presence of expressions and measurement errors. Work flows with examples for simulation, estimation and prediction processes are also provided with parallelization speedup. The whole framework is tested with yeast genome and gene expression data of Yassour (2009).

Install the latest version of this package by entering the following in R:
install.packages("cubfits")
AuthorWei-Chen Chen [aut, cre], Russell Zaretzki [aut], William Howell [aut], Cedric Landerer [aut], Drew Schmidt [aut], Michael A. Gilchrist [aut], Preston Hewgley [ctb], Students REU13 [ctb]
Date of publication2016-01-24 21:39:07
MaintainerWei-Chen Chen <wccsnow@gmail.com>
LicenseMozilla Public License 2.0
Version0.1-2
https://github.com/snoweye/cubfits

View on CRAN

Functions

AllDataFormats Man page
asl.optim Man page
b Man page
b.Init Man page
bVec Man page
calc_cai_values Man page
calc_scuo_values Man page
calc_scu_values Man page
.CF.AC Man page
.CF.CONF Man page
.CF.CT Man page
.CF.DP Man page
.CF.GV Man page
.CF.OP Man page
.CF.PARAM Man page
.CF.PT Man page
.CO.CT Man page
codon.low2up Man page
codon.up2low Man page
convert.b.to.bVec Man page
convert.bVec.to.b Man page
convert.n.to.list Man page
convert.reu13.df.to.list Man page
convert.seq.data.to.string Man page
convert.y.to.list Man page
convert.y.to.scuo Man page
cp.workflow Man page
cubappr Man page
cubfits Man page
.cubfitsEnv Man page
cubfits-package Man page
cubmultichain Man page
cubpred Man page
cubsinglechain Man page
dasl Man page
dasla Man page
DataConverting Man page
DataGenerating Man page
DataIO Man page
dmixnormerr Man page
dna.low2up Man page
dna.up2low Man page
estimatePhi Man page
ex.test Man page
ex.train Man page
fitMultinom Man page
gen.n Man page
gen.phi.Obs Man page
gen.reu13.df Man page
gen.reu13.list Man page
gen.scuo Man page
gen.y Man page
get.expath Man page
get.workflow Man page
init.function Man page
isConverged Man page
mixnormerr.optim Man page
n Man page
n.list Man page
normalizeDataSet Man page
pasl Man page
pasla Man page
phi.df Man page
phi.Obs Man page
plotaddmodel Man page
plotbin Man page
plotbin.NSE Man page
plotBMatrixPosterior Man page
plotCUB Man page
plotCUB.NSE Man page
plotExpectedPhiTrace Man page
plotmodel Man page
plotprxy Man page
plotPTraces Man page
plotTraces Man page
print.mixnormerr Man page
prop.bin.roc Man page
prop.model.nse Man page
prop.model.roc Man page
qasl Man page
qasla Man page
rasl Man page
rasla Man page
readGenome Man page
read.phi.df Man page
read.seq Man page
rearrange.n Man page
rearrange.phi.Obs Man page
rearrange.reu13.df Man page
rearrange.y Man page
reu13.df Man page
reu13.list Man page
scuo Man page
scuo.random Man page
seq.data Man page
seq.string Man page
simu.mixnormerr Man page
simu.orf Man page
simu.phi.Obs Man page
write.phi.df Man page
write.seq Man page
y Man page
yassour Man page
yassour.info Man page
yassour.PM.appr Man page
yassour.PM.fits Man page
y.list Man page

Files

COPYING
inst
inst/CITATION
inst/ex_data
inst/ex_data/seq_200.fasta
inst/ex_data/phi_200.tsv
inst/doc
inst/doc/cubfits-guide.Rnw
inst/doc/cubfits-guide.pdf
inst/workflow
inst/workflow/00_readme.txt
inst/workflow/param
inst/workflow/param/small_bInit.rda
inst/workflow/param/small_length.rda
inst/workflow/param/small_train.rda
inst/workflow/roc
inst/workflow/roc/00_readme.txt
inst/workflow/roc/code
inst/workflow/roc/code/02-get_data.r inst/workflow/roc/code/01-mkdir_output.r inst/workflow/roc/code/s1-generate_data.r inst/workflow/roc/code/04-wophi_scuo-tp.r inst/workflow/roc/code/00-set_env_wphi.r inst/workflow/roc/code/s4-wphi_true-tp.r inst/workflow/roc/code/04-wphi_pm-tp.r inst/workflow/roc/code/04-wophi_pm-tp.r inst/workflow/roc/code/03-get_init-tp.r inst/workflow/roc/code/00-set_env_wophi.r inst/workflow/roc/code/u1-get_negsel.r inst/workflow/roc/code/05-subset-tp.r inst/workflow/roc/code/00-set_env_wphi_wophi.r inst/workflow/roc/code/00-set_env_simu.r inst/workflow/roc/code/s4-wophi_true-tp.r inst/workflow/roc/code/04-wphi_scuo-tp.r inst/workflow/roc/code/04-wphi_wophi_pm-tp.r inst/workflow/roc/code/04-wphi_wophi_scuo-tp.r
inst/workflow/roc/01_code.txt
inst/workflow/roc/code_plot_ps
inst/workflow/roc/code_plot_ps/u6-adjust_focal_codon.r inst/workflow/roc/code_plot_ps/m6-plot_prxy_wci.r inst/workflow/roc/code_plot_ps/06-plotsingle_prxy.r inst/workflow/roc/code_plot_ps/07-plotdiag_bin.r inst/workflow/roc/code_plot_ps/s6-plotsingle_model_true.r inst/workflow/roc/code_plot_ps/m6-plot_b_corr_negsel.r inst/workflow/roc/code_plot_ps/s6-plotsingle_prxy_true.r inst/workflow/roc/code_plot_ps/s6-plotsingle_mscu.r inst/workflow/roc/code_plot_ps/s6-plotsingle_prxy_true_wci.r inst/workflow/roc/code_plot_ps/m7-plot_bin.r inst/workflow/roc/code_plot_ps/s7-plotaa_deltat_true.r inst/workflow/roc/code_plot_ps/07-plotdiag_EPhi_hist.r inst/workflow/roc/code_plot_ps/05-subset_tsv.r inst/workflow/roc/code_plot_ps/u5-new_page.r inst/workflow/roc/code_plot_ps/07-plottrace_quantile_Phi.r inst/workflow/roc/code_plot_ps/08-plotmulti_wophi_wphi.r inst/workflow/roc/code_plot_ps/s8-plotmulti_true.r inst/workflow/roc/code_plot_ps/06-plotsingle_model.r inst/workflow/roc/code_plot_ps/s6-plotsingle_scu_mscu.r inst/workflow/roc/code_plot_ps/u2-plot_b_corr.r inst/workflow/roc/code_plot_ps/u0-get_case_main.r inst/workflow/roc/code_plot_ps/u3-plot_trace.r inst/workflow/roc/code_plot_ps/07-plottrace_logL-tp.r inst/workflow/roc/code_plot_ps/m6-plot_prxy.r inst/workflow/roc/code_plot_ps/u4-plot_aa_allinone.r inst/workflow/roc/code_plot_ps/s6-plotsingle_b_corr_true.r inst/workflow/roc/code_plot_ps/m6-plot_b_corr.r inst/workflow/roc/code_plot_ps/06-plotsingle_prxy_wci.r inst/workflow/roc/code_plot_ps/07-plotdiag_acceptvsEPhi.r
inst/workflow/roc/script
inst/workflow/roc/script/wphi_wophi_run_0.sh
inst/workflow/roc/script/wphi_wophi_run_2.sh
inst/workflow/roc/script/simu_run_2_ps.sh
inst/workflow/roc/script/simu_run_0.sh
inst/workflow/roc/script/simu_run_1.sh
inst/workflow/roc/script/wophi_run_2_ps.sh
inst/workflow/roc/script/simu_run_2.sh
inst/workflow/roc/script/wphi_run_0.sh
inst/workflow/roc/script/wphi_wophi_run_1.sh
inst/workflow/roc/script/wphi_run_1.sh
inst/workflow/roc/script/wphi_wophi_run_2_ps.sh
inst/workflow/roc/script/wophi_run_2.sh
inst/workflow/roc/script/wophi_run_1.sh
inst/workflow/roc/script/wphi_run_2.sh
inst/workflow/roc/script/wophi_run_0.sh
inst/workflow/roc/script/wphi_run_2_ps.sh
inst/workflow/roc/code_plot
inst/workflow/roc/code_plot/u6-adjust_focal_codon.r inst/workflow/roc/code_plot/07-plotdiag_scuo_cai.r inst/workflow/roc/code_plot/m6-plot_prxy_wci.r inst/workflow/roc/code_plot/06-plotsingle_prxy.r inst/workflow/roc/code_plot/07-plotdiag_accept_hist.r inst/workflow/roc/code_plot/07-plotdiag_bin.r inst/workflow/roc/code_plot/s6-plotsingle_model_true.r inst/workflow/roc/code_plot/s3-plotdiag_bin_est.r inst/workflow/roc/code_plot/03-plotdiag_init.r inst/workflow/roc/code_plot/m6-plot_b_corr_negsel.r inst/workflow/roc/code_plot/s6-plotsingle_prxy_true.r inst/workflow/roc/code_plot/s6-plotsingle_mscu.r inst/workflow/roc/code_plot/s6-plotsingle_prxy_true_wci.r inst/workflow/roc/code_plot/m7-plot_bin.r inst/workflow/roc/code_plot/s7-plotaa_deltat_true.r inst/workflow/roc/code_plot/07-plotdiag_EPhi_hist.r inst/workflow/roc/code_plot/07-plotdiag_sigmaW_hist.r inst/workflow/roc/code_plot/s1-plotdiag_simu_phi.r inst/workflow/roc/code_plot/05-subset_tsv.r inst/workflow/roc/code_plot/u5-new_page.r inst/workflow/roc/code_plot/07-plottrace_quantile_Phi.r inst/workflow/roc/code_plot/08-plotmulti_wophi_wphi.r inst/workflow/roc/code_plot/s8-plotmulti_true.r inst/workflow/roc/code_plot/06-plotsingle_model.r inst/workflow/roc/code_plot/s6-plotsingle_scu_mscu.r inst/workflow/roc/code_plot/u2-plot_b_corr.r inst/workflow/roc/code_plot/u0-get_case_main.r inst/workflow/roc/code_plot/u3-plot_trace.r inst/workflow/roc/code_plot/07-plottrace_prior.r inst/workflow/roc/code_plot/07-plottrace_logL-tp.r inst/workflow/roc/code_plot/m6-plot_prxy.r inst/workflow/roc/code_plot/07-plottrace_param_meanEPhi.r inst/workflow/roc/code_plot/u4-plot_aa_allinone.r inst/workflow/roc/code_plot/s6-plotsingle_b_corr_true.r inst/workflow/roc/code_plot/03-plotdiag_bin_est.r inst/workflow/roc/code_plot/07-plotdiag_medPhi_EPhi.r inst/workflow/roc/code_plot/m6-plot_b_corr.r inst/workflow/roc/code_plot/06-plotsingle_prxy_wci.r inst/workflow/roc/code_plot/s2-plotdiag_bin_true.r inst/workflow/roc/code_plot/07-plotdiag_acceptvsEPhi.r
configure.ac
src
src/lib.c
src/lp_c_raw.c
src/stable_exp.c
NAMESPACE
demo
demo/roc.appr.r demo/fitMultinom.r demo/roc.simu.r demo/scuo.r demo/plotbin.r demo/roc.pred.r demo/cai.r
demo/00Index
demo/basic.r demo/roc.train.r demo/yassour.asl.r demo/mSCU.r demo/yassour.mixture.r demo/yassour.mixed.r
INSTALL
data
data/yassour.mcmc.rda
data/b.Init.rda
data/plot.r
data/ex.train.rda
data/yassour.rda
data/control.r data/control_optim.r data/envir.r data/global.r
data/ex.test.rda
R
R/index.scuo.r R/dsn.logmixture.r R/my.stop.r R/plotcolor.r R/my.objectivePhiOne.nlogphiL.r R/my.drawBConditionalAll.r R/plotprxy.r R/my.objectivePhiOne.phiLfp.r R/my.fitMultinomAll.r R/workflow.create.r R/data.gen.n.r R/my.drawPhiConditionalAllPred.r R/index.scuo.random.r R/prop.model.nse.r R/000_globalVariables.r R/my.fitMultinomOne.r R/asl.probability.r R/cedric.convergence.r R/cedric.plotting.r R/my.check.data.r R/data.gen.phi.Obs.r R/logan.plotting.r R/my.adaptive.r R/my.util.r R/my.cat.r R/my.logPosteriorAllPred.r R/my.logLAllPred.r R/simu.phi.Obs.r R/my.logdmultinomCodAll.r R/my.estimatePhiAll.r R/asl.random.r R/my.pPropTypeNoObs.logmixture.r R/my.drawbiasPhi.r R/my.proposesigmaPhi.r R/my.drawBConditionalFit.r R/data.io.r R/workflow.get.expath.r R/data.codon.convert.r R/mixnormerr.optim.r R/my.proposePhiAllPred.r R/asl.quantile.r R/data.gen.reu13.list.r R/my.pPropType.lognormal_RW.r R/plotbin.r R/my.logPosteriorAll.r R/plotmodel.r R/my.pPropTypeNoObs.lognormal_bias.r R/my.drawPhiConditionalAll.r R/my.logdmultinomCodOne.r R/my.proposeB.r R/data.gen.reu13.df.r R/data.convert.r R/my.objectivePhiOne.nlogL.r R/my.pPropType.logmixture.r R/my.dump.r R/my.init_param.r R/my.coef.r R/my.adaptive.DrawScale.r R/my.objectivePhiOne.Lfp.r R/zzz.r R/my.verbose.r R/my.drawRestrictHP.r R/my.cubfits.r R/my.init.r R/prop.bin.roc.r R/asl.optim.r R/prop.model.roc.r R/my.acceptance.r R/data.gen.y.r R/data.rearrange.r R/my.print.r R/asl.density.r R/simu.orf.r R/index.scu.r R/my.logLAll.r R/index.cai.r R/my.pPropType.r R/my.pPropType.lognormal_bias.r R/yyy.r R/cedric.io.r R/my.pPropTypeNoObs.lognormal_RW.r R/index.gen.scuo.r R/my.pPropTypeNoObs.r R/simu.mixnormerr.r R/dsn.dirichlet.r R/cedric.mapBMatNames.r R/my.proposePhiAll.r R/my.proposebiasPhi.r R/my.check.rearrange.r R/my.cubpred.r R/my.cubappr.r R/my.inverse.mlogit.r R/my.estimatePhiOne.r
vignettes
vignettes/cubfits-guide.Rnw
vignettes/build_pdf.sh
vignettes/cubfits-include
vignettes/cubfits-include/07-misc.tex
vignettes/cubfits-include/00-preamble.tex
vignettes/cubfits-include/05-utilities.tex
vignettes/cubfits-include/01-acknowledgement.tex
vignettes/cubfits-include/06-faq.tex
vignettes/cubfits-include/01-copyright.tex
vignettes/cubfits-include/01-introduction.tex
vignettes/cubfits-include/04-workflows.tex
vignettes/cubfits-include/03-speedup.tex
vignettes/cubfits-include/figure
vignettes/cubfits-include/figure/workflows.pdf
vignettes/cubfits-include/figure/more_asl.pdf
vignettes/cubfits-include/figure/more_mixture.pdf
vignettes/cubfits-include/figure/prxy_roc_ad_appr_pm_5k-10k.pdf
vignettes/cubfits-include/figure/plotbin.pdf
vignettes/cubfits-include/figure/prxy_roc_ad_fits_pm_5k-10k.pdf
vignettes/cubfits-include/figure/avg_run_time.pdf
vignettes/cubfits-include/figure/fitMultinom.pdf
vignettes/cubfits-include/figure/bayesian_model.pdf
vignettes/cubfits-include/cubfits.bib
vignettes/cubfits-include/my_jss.cls
vignettes/cubfits-include/02-main_functions.tex
MD5
README
DESCRIPTION
configure
ChangeLog
man
man/t1_simulation.Rd man/yy_yassour.Rd man/c0_plot.Rd man/a3_cubpred.Rd man/t4_cai.Rd man/yy_dataset.Rd man/u2_convert.Rd man/vv_print.Rd man/s1_fitMultinom.Rd man/t2_scuo.Rd man/b0_plotprxy.Rd man/s0_init.function.Rd man/t5_scu.Rd man/xx_dataformat.Rd man/u4_asl.Rd man/yy_control.Rd man/yy_yassour_PM.Rd man/b1_plotbin.Rd man/a1_cubfits.Rd man/c9_internal.Rd man/u1_gen.Rd man/c1_io.Rd man/u5_mixnorm.Rd man/00_cubfits-package.Rd man/u0_io.Rd man/zz_internal.Rd man/u3_rearrange.Rd man/c2_convergence.Rd man/s2_estimatePhi.Rd man/a2_cubappr.Rd man/t3_scuo.random.Rd man/b2_plotmodel.Rd
configure.win
cleanup

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