massdash.loaders.OpenSwathXICParquetLoader

class massdash.loaders.OpenSwathXICParquetLoader(**kwargs)

Bases: GenericChromatogramLoader

Class for loading Chromatograms and peak features from XIC (PyProphet) parquet files and a results files. Inherits from GenericChromatogramLoader

loadTransitionGroups(pep_id: str, charge: int, runNames: None | str | List[str] = None) → Dict[str, TransitionGroupCollection]

Loads the transition group for a given peptide ID and charge across all files :param pep_id: Peptide ID :type pep_id: str :param charge: Charge :type charge: int :param runNames: Name of the run to extract the transition group from. If None, all runs are extracted. If str, only the specified run is extracted. If List[str], only the specified runs are extracted. :type runNames: None | str | List[str]

Returns:

Dictionary of TransitionGroups, with keys as sqMass filenames

Return type:

Dict[str, TransitionGroup]

loadTransitionGroupsDf(pep_id: str, charge: int) → DataFrame

Loads the transition group for a given peptide ID and charge across all files into a pandas DataFrame

Parameters:

• pep_id (str) – Peptide ID

• charge (int) – Charge

Returns:

DataFrame containing TransitionGroup information across all runs

Return type:

pd.DataFrame