sctk.calculate_qc

sctk.calculate_qc(adata, flags={'hb': '^HB', 'mito': '^MT-', 'ribo': '^RP[LS]'}, extra_flags={}, flag_only=False, suffix='', **kwargs) → None

Calculate quality control (QC) metrics for an AnnData object. The object is modified in-place.

Parameters:

• adata – AnnData object to calculate QC metrics for.

• flags – Dictionary of QC flags and regular expression patterns to match gene names against.

• extra_flags – Additional QC flags and patterns to add to flags.

• flag_only – If True, only calculate QC flags and do not calculate other metrics.

• suffix – Suffix to append to QC metric names.

• **kwargs – Additional keyword arguments to pass to scanpy.pp.calculate_qc_metrics().

Returns:

None.

Raises:

None. –

Examples

>>> import scanpy as sc
>>> import sctk
>>> adata = sc.datasets.pbmc3k()
>>> sctk.calculate_qc(adata)