Pre-scan multiple h5ad files for multi-sample loading

Pre-scan multiple h5ad files for multi-sample loading

Usage

prescan_h5ad_files(
  h5_paths,
  gene_universe = c("intersection", "union"),
  var_index = "_index"
)

Arguments

h5_paths

Character vector of file paths to h5ad files. If names are provided, these will be used as experimental identifiers.

gene_universe

One of "intersection" or "union".

var_index

String. The name within the h5ad var part in which the variable names are stored. Defaults to "_index".

Value

A list with:

• universe - Character vector of gene names in the universe

• file_tasks - List of per-file task structures, each containing: exp_id, h5_path, cs_type, no_cells, no_genes, gene_local_to_universe (integer vector, NA for genes not in universe, 0-indexed into universe)