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).

Author
Wei-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 publication
2016-01-24 21:39:07
Maintainer
Wei-Chen Chen <wccsnow@gmail.com>
License
Mozilla Public License 2.0
Version
0.1-2
URLs

View on CRAN

Man pages

00_cubfits-package
Codon Bias Usage Fits
a1_cubfits
Codon Usage Bias Fits for Observed ORFs and Expression
a2_cubappr
Codon Usage Bias Approximation for ORFs without Expression
a3_cubpred
Codon Usage Bias Prediction for Observed ORFs
b0_plotprxy
Predictive X-Y Plot
b1_plotbin
Plot Binning Results
b2_plotmodel
Plot Fitted Models
c0_plot
Cedric Plot Utilities
c1_io
Cedric IO Utilities
c2_convergence
Cedric Convergence Utilities
c9_internal
All Cedric Internal Functions
s0_init.function
Initial Generic Functions of Codon Usage Bias Fits
s1_fitMultinom
Fit Multinomial Model (Generic)
s2_estimatePhi
Initialization of Phi (Generic)
t1_simulation
Simulate ORFs and Expression Data
t2_scuo
Function for Synonymous Codon Usage Order (SCUO) Index
t3_scuo.random
Generate Randomized SCUO Index
t4_cai
Function for Codon Adaptation Index (CAI)
t5_scu
Function for Selection on Codon Usage (SCU)
u0_io
Input and Output Utility
u1_gen
Generating Data Structure
u2_convert
Convert Data Frame to Other Formats
u3_rearrange
Rearrange Data Structure by ORF Names
u4_asl
The Asymmetric Laplace Distribution
u5_mixnorm
Mixed Normal Optimization
vv_print
Functions for Printing Objects According to Classes
xx_dataformat
Data Formats
yy_control
Default Controlling Options
yy_dataset
Datasets for Demonstrations
yy_yassour
Yassour 2009 Yeast Experiment Dataset
yy_yassour_PM
Posterior Results of Yassour 2009 Yeast Experiment Dataset
zz_internal
All Internal Functions

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