grassp.pp.filter_samples

filter_samples(data, *, min_counts=None, min_proteins=None, max_counts=None, max_proteins=None, inplace=True, copy=False)

Filter samples based on number of counts or proteins.

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 Optional[int] (default: None)

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

min_proteins Optional[int] (default: None)

Minimum number of proteins expressed required for a sample to pass filtering.

max_counts Optional[int] (default: None)

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

max_proteins Optional[int] (default: None)

Maximum number of proteins expressed required for a sample to pass filtering.

inplace bool (default: True)

Perform computation inplace or return result.

copy bool (default: False)

If an AnnData is passed, determines whether a copy is returned.

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_samples, retained_proteins) if input is not AnnData