Codon Usage Bias Fits


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Documentation for package ‘cubfits’ version 0.1-3

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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