OpenSwathScoring#

class pyopenms.OpenSwathScoring#

Bases: object

Cython implementation of _OpenSwathScoring

Original C++ documentation is available here

__init__()#

Overload:

__init__(self) → None

Overload:

__init__(self, in_0: OpenSwathScoring) → None

Methods

__init__

getNormalized_library_intensities_(self, ...)

initialize(self, rt_normalization_factor, ...)

Initialize the scoring object
getNormalized_library_intensities_(self, transitions: List[LightTransition], normalized_library_intensity: List[float]) → None#
initialize(self, rt_normalization_factor: float, add_up_spectra: int, spacing_for_spectra_resampling: float, merge_spectra_by_peak_width_fraction: float, drift_extra: float, su: OpenSwath_Scores_Usage, spectrum_addition_method: bytes, spectrum_merge_method_type: bytes, use_ms1_ion_mobility: bool, apply_im_peak_picking: bool) → None#

Initialize the scoring object

Sets the parameters for the scoring

Parameters:

  • rt_normalization_factor – Specifies the range of the normalized retention time space

  • add_up_spectra – How many spectra to add up (default 1)

  • spacing_for_spectra_resampling – Spacing factor for spectra addition

  • merge_spectra_by_peak_width_fraction – Fraction of peak width to construct the number of spectra to add

  • drift_extra – Extend the extraction window to gain a larger field of view beyond drift_upper - drift_lower (in percent)

  • su – Which scores to actually compute

  • spectrum_addition_method – Method to use for spectrum addition (valid: “simple”, “resample”)

  • spectrum_merge_method_type – Type of method to use for spectrum addition. (valid: “fixed”, “dynamic”)

  • use_ms1_ion_mobility – Use MS1 ion mobility extraction in DIA scores

  • apply_im_peak_picking – Apply peak picking to the extracted ion mobilograms