snapatac2.pp.make_peak_matrix#

snapatac2.pp.make_peak_matrix(adata, file=None, use_rep='peaks', peak_file=None, chunk_size=500)[source]#

Generate cell by peak count matrix.

This function will generate a cell by peak count matrix and store it in a new .h5ad file.

import_data() must be ran first in order to use this function.

Parameters

  • adata (AnnData | AnnDataSet) – The (annotated) data matrix of shape n_obs x n_vars. Rows correspond to cells and columns to regions.

  • file (Optional[Path]) – 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.

  • use_rep (str | list[str]) – This is used to read peak information from .uns[use_rep]. The peaks can also be provided by a list of strings: [“chr1:1-100”, “chr2:2-200”].

  • peak_file (Optional[Path]) – Bed file containing the peaks. If provided, peak information will be read from this file.

  • chunk_size (int) – Chunk size

Returns

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

Return type

AnnData | ad.AnnData