Extract the primary count matrix from an AnnData object

Selects a layer from `adata$layers` if `layer` is supplied and present; otherwise falls back to `adata$X`. The returned matrix is in AnnData orientation (cells x features) and converted to CsparseMatrix. Row and column names are set from `obs_names` / `var_names` when provided.

Usage

extract_anndata_X(adata, layer = NULL, obs_names = NULL, var_names = NULL)

Arguments

adata

An AnnData object.

layer

Optional name of a layer in `adata$layers` to use as the primary matrix. If `NULL` or missing, `adata$X` is used.

obs_names

Character vector of cell names (rows). Optional.

var_names

Character vector of feature names (columns). Optional.

Value

A CsparseMatrix of shape `n_obs x n_vars` (cells x features).