grassp.pp.filter_min_consecutive_fractions

filter_min_consecutive_fractions(data, min_consecutive=2, replicate_column=None, min_replicates=None, inplace=True)

Filters for proteins present in at least min_consecutive of specified consecutive fractions.

Parameters:

data AnnData

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

min_consecutive int

Minimum number of consecutive fractions in which a protein must be detected to pass filtering.

replicate_column str, optional

Column name in data.obs that contains replicate identifiers. If provided, consecutive fraction filtering is applied per replicate, and proteins must meet the min_consecutive threshold in at least min_replicates number of replicates. If None, filtering is applied across all samples as a single dataset.

min_replicates int, optional

Minimum number of replicates that must satisfy the consecutive fraction requirement for a protein to be retained.

inplace bool, default True

If True, modifies the input AnnData object in place and returns None. If False, returns a new filtered AnnData object.

Return type:

ndarray | None

Returns:

Depending on inplace and input type, returns either:

None

if inplace=True

np.ndarray

A boolean mask of proteins that passed the filter, if inplace=False.