betareg_optimize: Optimize Beta regression negative log likelihood function

Description Usage Arguments Value Author(s) See Also

Description

The function betareg_optimize minimizes the negative log likelihood of the Beta regression model Since it cannot be evaluated analytically, an optimization procedure is used. The optim packages is used for performing optimization.

Usage

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betareg_optim(x, ...)

## S3 method for class 'list'
betareg_optim(x, w = NULL, disp = 1, basis = NULL,
  fit_feature = "RMSE", cpg_dens_feat = TRUE, lambda = 1/2,
  opt_method = "CG", opt_itnmax = 100, is_parallel = TRUE,
  no_cores = NULL, ...)

## S3 method for class 'matrix'
betareg_optim(x, w = NULL, disp = 1, basis = NULL,
  fit_feature = "RMSE", cpg_dens_feat = TRUE, lambda = 1/2,
  opt_method = "CG", opt_itnmax = 100, ...)

Arguments

x

The input object, either a matrix or a list.

...

Additional parameters.

w

A vector of parameters (i.e. coefficients of the basis functions)

disp

Dispersion parameter/vector for Beta distribution

basis

A 'basis' object. E.g. see create_rbf_object.

fit_feature

Return additional feature on how well the profile fits the methylation data. Either NULL for ignoring this feature or one of the following: 1) "RMSE" for returning the fit of the profile using the RMSE as measure of error or 2) "NLL" for returning the fit of the profile using the Negative Log Likelihood as measure of error.

cpg_dens_feat

Logical, whether to return an additional feature for the CpG density across the promoter region.

lambda

The complexity penalty coefficient for ridge regression.

opt_method

The optimization method to be used. See optim for possible methods. Default is "CG".

opt_itnmax

Optional argument giving the maximum number of iterations for the corresponding method. See optim for details.

is_parallel

Logical, indicating if code should be run in parallel.

no_cores

Number of cores to be used, default is max_no_cores - 2.

Value

Depending on the input object x:

Author(s)

C.A.Kapourani C.A.Kapourani@ed.ac.uk

See Also

create_basis, eval_functions


andreaskapou/BPRMeth-devel documentation built on May 12, 2019, 3:32 a.m.