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).

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

Files in this package

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

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