simba.pp.cal_qc_atac

simba.pp.cal_qc_atac(adata, expr_cutoff=1)

Calculate quality control metrics.

Parameters:

• adata (AnnData) – Annotated data matrix.

• expr_cutoff (float, optional (default: 1)) – Expression cutoff. If greater than expr_cutoff,the feature is considered ‘expressed’

• assay (str, optional (default: ‘rna’)) – Choose from {‘rna’,’atac’},case insensitive

Returns:

• updates adata with the following fields.

• n_counts (pandas.Series (adata.var[‘n_counts’],dtype int)) – The total read count for a peak.

• n_cells (pandas.Series (adata.var[‘n_cells’],dtype int)) – The total number of cells which have at least one peak.

• pct_cells (pandas.Series (adata.var[‘pct_cells’],dtype float)) – The percentage of cells which have at least one peak.

• n_counts (pandas.Series (adata.obs[‘n_counts’],dtype int)) – The total read count for a cell.

• n_peaks (pandas.Series (adata.obs[‘n_peaks’],dtype int)) – The number of peaks that are present in each cell.

• pct_peaks (pandas.Series (adata.obs[‘pct_peaks’],dtype int)) – The percentage of peaks that are present in each cell.