cellink.pp.variant_qc

cellink.pp.variant_qc(adata, *, maf_threshold=0.01, hwe_pval_threshold=1e-06, inplace=True, copy=False)

Perform quality control on variants.

This function filters variants based on Minor Allele Frequency (MAF) and Hardy-Weinberg Equilibrium (HWE).

Params

adata

The annotated data matrix of shape n_obs × n_vars.

maf_threshold

The threshold for minor allele frequency (MAF).

hwe_pval_threshold

The threshold for Hardy-Weinberg equilibrium (HWE) p-value.

inplace

Whether to update adata or return a copy of the new AnnData object.

copy

Whether to modify copied input object. Not compatible with inplace=False.

rtype:

AnnData | None

returns:

Returns the AnnData object with filtered variants or updates the input adata if inplace is True.