opt_esvd.eSVD: Optimize eSVD for eSVD objects

In linnykos/eSVD2: eSVD2 for performing the eSVD-DE for cohort-wide differential expression analysis

Optimize eSVD for eSVD objects

Description

Optimize eSVD for eSVD objects

Usage

## S3 method for class 'eSVD'
opt_esvd(
  input_obj,
  fit_name = "fit_First",
  fit_previous = "fit_Init",
  l2pen = 0.1,
  max_iter = 100,
  offset_variables = NULL,
  tol = 1e-06,
  verbose = 0,
  ...
)

Arguments

input_obj	eSVD object outputed from apply_initial_threshold.
fit_name	String for the name of that will become the current fit when storing the results in input_obj.
fit_previous	String for the name of the previous fit that this function will grab the initialization values from.
l2pen	Small positive number for the amount of penalization for both the cells' and the genes' latent vectors as well as the coefficients.
max_iter	Positive integer for number of iterations.
offset_variables	A vector of strings depicting which column names in input_obj$covariate be treated as an offset during the optimization (i.e., their coefficients will not change throughout the optimization).
tol	Small positive number to differentiate between zero and non-zero.
verbose	Integer.
...	Additional parameters.

Value

eSVD object with added elements with name to whatever fit_name was set to.

linnykos/eSVD2 documentation built on July 17, 2024, 12:01 a.m.