Codon Usage Bias Fits
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Documentation for package ‘cubfits’ version 0.1-4
- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Code demos. Use demo() to run them.
Help Pages
A B C D E F G I M N P Q R S W Y misc
| cubfits-package | Codon Bias Usage Fits |
-- A --
| AllDataFormats | Data Formats |
| asl.optim | The Asymmetric Laplace Distribution |
-- B --
| b | Data Formats |
| b.Init | Datasets for Demonstrations |
| bVec | Data Formats |
-- C --
| calc_cai_values | Function for Codon Adaptation Index (CAI) |
| calc_scuo_values | Function for Synonymous Codon Usage Order (SCUO) Index |
| calc_scu_values | Function for Selection on Codon Usage (SCU) |
| codon.low2up | Convert Data Frame to Other Formats |
| codon.up2low | Convert Data Frame to Other Formats |
| convert.b.to.bVec | Convert Data Frame to Other Formats |
| convert.bVec.to.b | Convert Data Frame to Other Formats |
| convert.n.to.list | Convert Data Frame to Other Formats |
| convert.reu13.df.to.list | Convert Data Frame to Other Formats |
| convert.seq.data.to.string | Convert Data Frame to Other Formats |
| convert.y.to.list | Convert Data Frame to Other Formats |
| convert.y.to.scuo | Convert Data Frame to Other Formats |
| cubappr | Codon Usage Bias Approximation for ORFs without Expression |
| cubfits | Codon Usage Bias Fits for Observed ORFs and Expression |
| cubmultichain | Cedric Convergence Utilities |
| cubpred | Codon Usage Bias Prediction for Observed ORFs |
| cubsinglechain | Cedric Convergence Utilities |
-- D --
| dasl | The Asymmetric Laplace Distribution |
| dasla | The Asymmetric Laplace Distribution |
| DataConverting | Convert Data Frame to Other Formats |
| DataGenerating | Generating Data Structure |
| DataIO | Input and Output Utility |
| dmixnormerr | Mixed Normal Optimization |
| dna.low2up | Convert Data Frame to Other Formats |
| dna.up2low | Convert Data Frame to Other Formats |
-- E --
| estimatePhi | Initialization of Phi (Generic) |
| ex.test | Datasets for Demonstrations |
| ex.train | Datasets for Demonstrations |
-- F --
| fitMultinom | Fit Multinomial Model (Generic) |
-- G --
| gen.n | Generating Data Structure |
| gen.phi.Obs | Generating Data Structure |
| gen.reu13.df | Generating Data Structure |
| gen.reu13.list | Generating Data Structure |
| gen.scuo | Generating Data Structure |
| gen.y | Generating Data Structure |
| get.expath | Input and Output Utility |
-- I --
| init.function | Initial Generic Functions of Codon Usage Bias Fits |
| isConverged | Cedric Convergence Utilities |
-- M --
| mixnormerr.optim | Mixed Normal Optimization |
-- N --
| n | Data Formats |
| n.list | Data Formats |
| normalizeDataSet | Cedric IO Utilities |
-- P --
| pasl | The Asymmetric Laplace Distribution |
| pasla | The Asymmetric Laplace Distribution |
| phi.df | Data Formats |
| phi.Obs | Data Formats |
| plotaddmodel | Plot Fitted Models |
| plotbin | Plot Binning Results |
| plotCUB | Cedric Plot Utilities |
| plotExpectedPhiTrace | Cedric Plot Utilities |
| plotmodel | Plot Fitted Models |
| plotprxy | Predictive X-Y Plot |
| plotPTraces | Cedric Plot Utilities |
| plotTraces | Cedric Plot Utilities |
| print.mixnormerr | Functions for Printing Objects According to Classes |
| prop.bin.roc | Plot Binning Results |
| prop.model.roc | Plot Fitted Models |
-- Q --
| qasl | The Asymmetric Laplace Distribution |
| qasla | The Asymmetric Laplace Distribution |
-- R --
| rasl | The Asymmetric Laplace Distribution |
| rasla | The Asymmetric Laplace Distribution |
| read.phi.df | Input and Output Utility |
| read.seq | Input and Output Utility |
| readGenome | Cedric IO Utilities |
| rearrange.n | Rearrange Data Structure by ORF Names |
| rearrange.phi.Obs | Rearrange Data Structure by ORF Names |
| rearrange.reu13.df | Rearrange Data Structure by ORF Names |
| rearrange.y | Rearrange Data Structure by ORF Names |
| reu13.df | Data Formats |
| reu13.list | Data Formats |
-- S --
| scuo | Data Formats |
| scuo.random | Generate Randomized SCUO Index |
| seq.data | Data Formats |
| seq.string | Data Formats |
| simu.mixnormerr | Simulate ORFs and Expression Data |
| simu.orf | Simulate ORFs and Expression Data |
| simu.phi.Obs | Simulate ORFs and Expression Data |
-- W --
| write.phi.df | Input and Output Utility |
| write.seq | Input and Output Utility |
-- Y --
| y | Data Formats |
| y.list | Data Formats |
| yassour | Yassour 2009 Yeast Experiment Dataset |
| yassour.info | Posterior Results of Yassour 2009 Yeast Experiment Dataset |
| yassour.PM.appr | Posterior Results of Yassour 2009 Yeast Experiment Dataset |
| yassour.PM.fits | Posterior Results of Yassour 2009 Yeast Experiment Dataset |
-- misc --
| .CF.AC | Default Controlling Options |
| .CF.CONF | Default Controlling Options |
| .CF.CT | Default Controlling Options |
| .CF.DP | Default Controlling Options |
| .CF.GV | Default Controlling Options |
| .CF.OP | Default Controlling Options |
| .CF.PARAM | Default Controlling Options |
| .CF.PT | Default Controlling Options |
| .CO.CT | Default Controlling Options |
| .cubfitsEnv | Default Controlling Options |