s1_fitMultinom: Fit Multinomial Model (Generic)

In cubfits: Codon Usage Bias Fits

Description

This generic function estimates b (mutation (log(mu)) and selection (Delta.t) parameters) depending on options set by init.function().

Usage

  fitMultinom(reu13.df, phi, y, n, phi.new = NULL, coefstart = NULL)

Arguments

reu13.df	an object of format reu13.df.
phi	an object of format phi.Obs.
y	an object of format y.
n	an object of format n.
phi.new	an object of format phi.Obs for MCMC only.
coefstart	initial value for b (mutation (log(mu)) and selection (Delta.t) parameters) only used in vglm().

Details

fitMultinom() fits a multinomial logistic regression via vector generalized linear model fitting, vglm(). By default, for each amino acids, the last codon (order by characters) is assumed as a based line, and other codons are compared to the based line relatively.

In MCMC, phi.new are new proposed expression values and used to propose new b. The coefstart is used to avoid randomization of estimating b in vglm(), and speed up computation.

Value

A list of format b is returned which are modified from the returns of vglm(). Mainly, it includes b$coefficient (parameters in vector), b$coef.mat (parameters in matrix), and b$R (covariance matrix of parameters, *R* matrix in QR decomposition).

Author(s)

Wei-Chen Chen [e-mail].

References

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

Shah P. and Gilchrist M.A. “Explaining complex codon usage patterns with selection for translational efficiency, mutation bias, and genetic drift” Proc Natl Acad Sci USA (2011) 108:10231–10236.

See Also

init.function() and estimatePhi().

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.