simba.pp.cal_qc_rna

simba.pp.cal_qc_rna(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 gene.

• n_cells (pandas.Series (adata.var[‘n_cells’],dtype int)) – The number of cells that express at least one gene.

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

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

• n_genes (pandas.Series (adata.obs[‘n_genes’],dtype int)) – The number of genes expressed in a cell.

• pct_genes (pandas.Series (adata.obs[‘pct_genes’],dtype float)) – The percentage of genes expressed in a cell.

• pct_mt (pandas.Series (adata.obs[‘pct_mt’],dtype float)) – the percentage of mitochondrial gene reads for a cell.