# Codon Usage Bias Fits

## 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