simba.pp.cal_qc

simba.pp.cal_qc(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 total read count for a feature.

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

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

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

  • n_features (pandas.Series (adata.obs[‘n_features’],dtype int)) – The number of features expressed in a sample.

  • pct_features (pandas.Series (adata.obs[‘pct_features’],dtype float)) – The percentage of features expressed in a sample.