grassp.pp.filter_proteins

filter_proteins(data, *, min_counts=None, min_samples=None, max_counts=None, max_samples=None, inplace=True, min_consecutive=None)

Filter proteins based on number of counts or samples.

Parameters:

data AnnData | spmatrix | ndarray | Array

The annotated data matrix of shape n_obs x n_vars. Rows correspond to proteins and columns to samples.

min_counts int | None (default: None)

Minimum number of counts required for a protein to pass filtering.

min_samples int | None (default: None)

Minimum number of samples expressed required for a protein to pass filtering.

max_counts int | None (default: None)

Maximum number of counts required for a protein to pass filtering.

max_samples int | None (default: None)

Maximum number of samples expressed required for a protein to pass filtering.

inplace bool (default: True)

Perform computation inplace or return result.

min_consecutive int | None (default: None)

(If using fractionation instead of organellar IP) Minimum number of consecutive fractions that a protein is present in.

Return type:

AnnData | tuple[ndarray, ndarray] | None

Returns:

Depending on inplace and input type, returns either:

• None if inplace=True

• AnnData if input is AnnData and inplace=False

• A tuple of arrays (retained_proteins, retained_samples) if input is not AnnData