simba.pp.cal_qc_rna
- simba.pp.cal_qc_rna(adata, expr_cutoff=1)[source]
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 number of read count each gene has.
n_cells (pandas.Series (adata.var[‘n_cells’],dtype int)) – The number of cells in which each gene is expressed.
pct_cells (pandas.Series (adata.var[‘pct_cells’],dtype float)) – The percentage of cells in which each gene is expressed.
n_counts (pandas.Series (adata.obs[‘n_counts’],dtype int)) – The number of read count each cell has.
n_genes (pandas.Series (adata.obs[‘n_genes’],dtype int)) – The number of genes expressed in each cell.
pct_genes (pandas.Series (adata.obs[‘pct_genes’],dtype float)) – The percentage of genes expressed in each cell.
n_peaks (pandas.Series (adata.obs[‘n_peaks’],dtype int)) – The number of peaks expressed in each cell.
pct_peaks (pandas.Series (adata.obs[‘pct_peaks’],dtype int)) – The percentage of peaks expressed in each cell.
pct_mt (pandas.Series (adata.obs[‘pct_mt’],dtype float)) – the percentage of counts in mitochondrial genes