proteobench.score.quantscoresPYE module#

Module containing plasma quantification score calculators (PYE - Plasma Year Edition).

class proteobench.score.quantscoresPYE.QuantScoresPYE(precursor_column_name: str, species_expected_ratio, species_dict: Dict[str, str])[source]#

Bases: QuantScoresHYE

Class for computing quantification scores for plasma benchmarking (PYE module).

This class inherits from QuantScoresHYE and extends it with plasma-specific metrics and calculations. It follows the same ScoreBase interface pattern but adds custom logic tailored for plasma quantification benchmarking.

Parameters:

  • precursor_column_name (str) – Name of the precursor column.

  • species_expected_ratio (dict) – Dictionary containing the expected ratios for each species.

  • species_dict (dict) – Dictionary containing the species names and their column mappings.

generate_intermediate(filtered_df: DataFrame, replicate_to_raw: dict) → DataFrame[source]#

Generate intermediate data structure for plasma quantification scores.

This method extends the parent class implementation with plasma-specific metric calculations.

Parameters:

  • filtered_df (pd.DataFrame) – DataFrame containing the filtered data.

  • replicate_to_raw (dict) – Dictionary containing the replicate to raw mapping.

Returns:

DataFrame containing the intermediate data structure with plasma-specific metrics.

Return type:

pd.DataFrame