s2_estimatePhi: Initialization of Phi (Generic)

In cubfits: Codon Usage Bias Fits

Description

This generic function estimates Phi (expression value) either by posterior mean (PM) or by maximum likelihood estimator (MLE) depending on options set by init.function().

Usage

  estimatePhi(fitlist, reu13.list, y.list, n.list,
    E.Phi = .CF.OP$E.Phi, lower.optim = .CF.OP$lower.optim,
    upper.optim = .CF.OP$upper.optim,
    lower.integrate = .CF.OP$lower.integrate,
    upper.integrate = .CF.OP$upper.integrate, control = list())

Arguments

fitlist	an object of format b.
reu13.list	an object of format reu13.list.
y.list	an object of format y.list.
n.list	an object of format n.list.
E.Phi	potential expected value of Phi.
lower.optim	lower bound to optim().
upper.optim	upper bound to optim().
lower.integrate	lower bound to integrate().
upper.integrate	upper bound to integrate().
control	control options to optim().

Details

estimatePhi() is a generic function first initialized by init.function(), then it estimates Phi accordingly. By default, .CF.CT$init.Phi sets the method PM for the posterior mean.

PM uses a flat prior and integrate() to estimate Phi. While, MLE uses optim() to estimate Phi which may have boundary solutions for some sequences.

Value

Estimated Phi for every sequence is returned.

Author(s)

Wei-Chen Chen [e-mail].

References

https://github.com/snoweye/cubfits/

See Also

init.function() and fitMultinom().

Examples

## Not run: 
suppressMessages(library(cubfits, quietly = TRUE))
set.seed(1234)

# Convert data.
reu13.list <- convert.reu13.df.to.list(ex.test$reu13.df)
y.list <- convert.y.to.list(ex.test$y)
n.list <- convert.n.to.list(ex.test$n)

# Get phi.pred.Init
init.function(model = "roc")
fitlist <- fitMultinom(ex.train$reu13.df, ex.train$phi.Obs, ex.train$y, ex.train$n)
phi.pred.Init <- estimatePhi(fitlist, reu13.list, y.list, n.list,
                         E.Phi = median(ex.test$phi.Obs),
                         lower.optim = min(ex.test$phi.Obs) * 0.9,
                         upper.optim = max(ex.test$phi.Obs) * 1.1)

## End(Not run)

cubfits documentation built on Nov. 8, 2021, 1:07 a.m.