metalsinglecell.pp.calculate_qc_metrics

metalsinglecell.pp.calculate_qc_metrics(adata, qc_vars=(), percent_top=None, log1p=True, layer=None, copy=False)

Per-cell/per-gene QC metrics (sc.pp.calculate_qc_metrics).

qc_vars (e.g. ['mt']) adds total_counts_<v>/pct_counts_<v> for each boolean adata.var[v] gene set; log1p adds log1p_* columns; percent_top (a list of N, default None) adds pct_counts_in_top_N_genes. The per-gene total lands in var['total_counts'] (scanpy’s name), matching sc.pp.calculate_qc_metrics.

Parameters:

• log1p (bool)

• copy (bool)