bpr_optim.list: Optimization method for the BPR NLL function using list x

In andreaskapou/mpgex: Methylation Profiles predict Gene Expression

Description

bpr_optim.list minimizes the negative log likelihood of the BPR function. Since it cannot be evaluated analytically, an optimization procedure is used. The optim packages is used for performing optimization. This method calls bpr_optim.matrix to process each element of the list.

Usage

## S3 method for class 'list'
bpr_optim(x, w = NULL, basis = NULL, fit_feature = NULL,
  cpg_dens_feat = FALSE, opt_method = "CG", opt_itnmax = 100,
  is_parallel = TRUE, no_cores = NULL, ...)

Arguments

x	A list of elements of length N, where each element is an L x 3 matrix of observations, where 1st column contains the locations. The 2nd and 3rd columns contain the total trials and number of successes at the corresponding locations, repsectively.
w	A vector of parameters (i.e. coefficients of the basis functions)
basis	A 'basis' object. See polynomial.object
fit_feature	Additional feature on how well the profile fits the methylation data.
cpg_dens_feat	Additional feature for the CpG density across the promoter region.
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 - 1.
...	Additional parameters

Value

A list containing the following elements:

• W_opt: An Nx(M+1) matrix with the optimized parameter values. Each row of the matrix corresponds to each element of the list x. The columns are of the same length as the parameter vector w (i.e. number of basis functions).

• Mus: An N x M matrix with the RBF centers if basis object is rbf.object, otherwise NULL.

• basis: The basis object.

• w: The initial values of the parameters w.

• x_extrema: The min and max values of each promoter region.

See Also

bpr_optim, bpr_optim.matrix

Examples

ex_data <- bpr_data
basis <- rbf.object(M=3)
out_opt <- bpr_optim(x = ex_data, is_parallel = TRUE, basis = basis, opt_method = "CG")

andreaskapou/mpgex documentation built on May 12, 2019, 3:33 a.m.