cellink.pp.low_abundance_filter

cellink.pp.low_abundance_filter(adata, *, abundance_threshold=1e-06, method='mean', inplace=True, copy=True)

Filter out low-abundance metabolites.

This function removes metabolites (features) with abundance below a specified threshold. Users can choose whether to filter based on the mean or median abundance across samples.

Parameters:

• adata (AnnData) – The annotated data matrix of shape n_obs x n_vars, where rows correspond to samples and columns to metabolites.

• abundance_threshold (float (default: 1e-06)) – The minimum abundance level to retain a metabolite. Features with abundance below this threshold will be filtered out.

• method (str (default: 'mean')) – Method to calculate abundance: “mean” or “median”.

• inplace (bool (default: True)) – Whether to update adata or return a copy of the new AnnData object.

• copy (bool (default: True)) – Whether to modify a copied input object. Not compatible with inplace=False.

Return type:

AnnData | None

Returns:

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