stereo.core.StPipeline.cal_qc

StPipeline.cal_qc(use_raw=True, layer=None)[source]

Calculate the key indicators of quality control.

Observation level metrics include:

  • total_counts: total number of counts for a cell.

  • n_genes_by_count: number of genes expressed of counts for a cell.

  • pct_counts_mt: percentage of total counts in a cell which are mitochondrial.

Parameters:

  • use_raw (Optional[bool]) – whether to use raw data, by default, use raw data if it exists.

  • layer (Optional[str]) – the key of layer to be used for calculating QC indicators, if gave, the use_raw will be ignored.

Return type:

A StereoExpData object storing quality control indicators, including two levels of obs (cell) and var (gene).