, min_features=100, min_cells=3, target_sum=None, n_top_features=100000, chunk_size=20000, backed=False, log=None)

Preprocessing single-cell ATAC-seq

  • adata (AnnData) – An AnnData matrice of shape n_obs x n_vars. Rows correspond to cells and columns to genes.

  • min_features (int) – Filtered out cells that are detected in less than n genes. Default: 100.

  • min_cells (int) – Filtered out genes that are detected in less than n cells. Default: 3.

  • target_sum – After normalization, each cell has a total count equal to target_sum. If None, total count of each cell equal to the median of total counts for cells before normalization. Default: None.

  • n_top_features – Number of highly-variable features to keep. Default: 30000.

  • chunk_size (int) – Number of samples from the same batch to transform. Default: 20000.

  • log – If log, record each operation in the log file. Default: None.

Return type:

The AnnData object after preprocessing.