cubfits (version 0.1-2)

Fit Multinomial: Fit Multinomial Model (Generic)

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().

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).

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.

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)