.quantify_proteoforms

proteopy.pp.quantify_proteoforms(adata, *, group_by='proteoform_id', layer=None, func='sum', proteodata_target_level='protein', inplace=True)

Aggregate intensities in adata.X (or selected layer) by .var[group_col], aggregate annotations in adata.var by concatenating unique values with ';', and set group_col as the new index (var_names).

Parameters:

• adata (AnnData) – Input AnnData with .X (obs x vars) and .var annotations.

• group_by (str) – Column in adata.var to group by (e.g. ‘protein_id’).

• layer (str, optional) – Key in adata.layers; when set, quantification uses that layer instead of adata.X.

• func ({'sum', 'median', 'max'} | Callable) – Aggregation to apply across grouped variables.

• proteodata_target_level ({'protein', 'peptide'} or None, optional) – Set the proteodata level of the output. When None the data level and columns are left as is. When 'protein', a protein_id column matching the new var index is added so the result satisfies protein-level proteodata requirements; any pre-existing protein_id column is renamed to protein_id_old and any peptide_id column is removed. When 'peptide', a peptide_id column matching the new var index is added so the result satisfies peptide-level proteodata requirements; a protein_id column must already exist in the inherited annotations.

• inplace (bool) – If True, modify adata in place; else return a new AnnData.

Returns:

Aggregated AnnData if inplace=False; otherwise None.

Return type:

AnnData | None