snapatac2.pp.import_values#

snapatac2.pp.import_values(input_dir, chrom_sizes, *, file=None, whitelist=None, chunk_size=200, backend='hdf5')[source]#

Import values associated with base pairs, typically from experiments like whole-genome bisulfite sequencing (WGBS).

Parameters:

input_dir (Path) – Directory containing the input files. Each file corresponds to a single cell.
chrom_sizes (Genome | dict[str, int]) – A Genome object or a dictionary containing chromosome sizes, for example, {"chr1": 2393, "chr2": 2344, ...}.
file (Path | None) – File name of the output h5ad file used to store the result. If provided, result will be saved to a backed AnnData, otherwise an in-memory AnnData is used.
whitelist (Path | list[str] | None) – File name or a list of barcodes. If it is a file name, each line must contain a valid barcode. When provided, only barcodes in the whitelist will be retained.
chunk_size (int) – Increasing the chunk_size speeds up I/O but uses more memory.
backend (Literal['hdf5']) – The backend.

Returns:

An annotated data matrix of shape n_obs x n_vars. Rows correspond to cells and columns to regions. If file=None, an in-memory AnnData will be returned, otherwise a backed AnnData is returned.

Return type:

AnnData | ad.AnnData