Multi-slide SkrCCA optimization - Multiple Components — optimize_bilinear_n_multi

Computes components 2 to nCC using deflation Uses flat kernel structure for consistent data access

Usage

optimize_bilinear_n_multi_slides(
  X_list_all,
  flat_kernels,
  sigma,
  slides,
  w_list,
  cellTypesOfInterest,
  nCC = 2,
  max_iter = 1000,
  tol = 1e-05,
  n_cores = 1,
  step_size = 1,
  sdev2_list = NULL
)

Arguments

X_list_all: List of lists of data matrices
flat_kernels: Flat list of kernel matrices
sigma: Sigma value (numeric)
slides: Slide IDs
w_list: Initial weight list with first component(s)
cellTypesOfInterest: Cell types to process
nCC: Total number of components desired
max_iter: Maximum iterations for refinement
tol: Convergence tolerance
n_cores: Number of cores for parallel computation
step_size: Step size for damped power iteration (default 1)
sdev2_list: Optional named list of squared standard deviations per cell type for weighted normalization. Default NULL.

Value

Updated weight list with all components