Description Usage Arguments Value See Also Examples
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.
1 2 3 4 |
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 |
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
|
opt_itnmax |
Optional argument giving the maximum number of iterations
for the corresponding method. See |
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 |
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.
1 2 3 | ex_data <- bpr_data
basis <- rbf.object(M=3)
out_opt <- bpr_optim(x = ex_data, is_parallel = TRUE, basis = basis, opt_method = "CG")
|
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