Extract layers from an AnnData object as a named list of matrices

Each layer is converted to CsparseMatrix and given dimnames from `obs_names` / `var_names`. The orientation is preserved as AnnData-native (cells x features); callers that need genes x cells (e.g. Seurat) should transpose.

Usage

extract_anndata_layers(
  adata,
  obs_names = NULL,
  var_names = NULL,
  exclude = character(0)
)

Arguments

adata

An AnnData object.

obs_names

Character vector of cell names.

var_names

Character vector of feature names.

exclude

Character vector of layer names to skip (e.g. one already used as the primary `X`).

Value

A named list of CsparseMatrix objects (cells x features). Empty list if the AnnData has no layers.