scalex.data.preprocessing_atac
- scalex.data.preprocessing_atac(adata, 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
- Parameters:
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.