massdash.peakPickers.MRMTransitionGroupPicker

class massdash.peakPickers.MRMTransitionGroupPicker(smoother, **kwargs)

Bases: object

python wrapper of the pyopenms MRMTransitionGroupPicker

getPrettyParameters() → Tuple

Get a list of current parameters and their values in a python friendly format Note: Changing the parameters will not update values

pick(transitionGroup: TransitionGroup) → List[TransitionGroupFeature]

Performs Peak Picking, Should return a TransitionGroupFeatureList object

setDefaults()

get the default parameters used by OpenSwath

setGeneralParameters(**kwargs)

Set a supported parameter

Parameters:

  • stop_after_feature (int) – Stop after feature

  • stop_after_intensity_ratio (float) – Stop after intensity ratio

  • min_peak_width (float) – Minimum peak width

  • recalculate_peaks_max_z (float) – Recalculate peaks max z

  • resample_boundary (float) – Resample boundary

  • recalculate_peaks (bool) – Recalculate peaks

  • background_subtraction (str) – Background subtraction

  • use_precursors (bool) – Use precursors

  • signal_to_noise (float) – Signal to noise

  • minimal_quality (float) – Minimal quality (if set, automatically sets compute_peak_quality to true)

setSmoother(smoother, sgolay_frame_length=11, sgolay_polynomial_order=3, gauss_width=50.0)

Set the smoother, can be one of [“original”, “guassian”, “sgolay”]