PeakIntegrator#

class pyopenms.PeakIntegrator#

Bases: object

Cython implementation of _PeakIntegrator

Original C++ documentation is available here: – Inherits from [‘DefaultParamHandler’]

Compute the area, background and shape metrics of a peak

The area computation is performed in integratePeak() and it supports integration by simple sum of the intensity, integration by Simpson’s rule implementations for an odd number of unequally spaced points or integration by the trapezoid rule

The background computation is performed in estimateBackground() and it supports three different approaches to baseline correction, namely computing a rectangular shape under the peak based on the minimum value of the peak borders (vertical_division_min), a rectangular shape based on the maximum value of the beak borders (vertical_division_max) or a trapezoidal shape based on a straight line between the peak borders (base_to_base)

Peak shape metrics are computed in calculatePeakShapeMetrics() and multiple metrics are supported

The containers supported by the methods are MSChromatogram and MSSpectrum

__init__()#

Overload:

__init__(self) → None

Overload:

__init__(self, in_0: PeakIntegrator) → None

Methods

`__init__`
`calculatePeakShapeMetrics`
`estimateBackground`
`getDefaultParameters`(self, in_0)
`getDefaults`(self)	Returns the default parameters
`getName`(self)	Returns the name
`getParameters`(self)	Returns the parameters
`getSubsections`(self)
`integratePeak`
`setName`(self, in_0)	Sets the name
`setParameters`(self, param)	Sets the parameters

calculatePeakShapeMetrics()#

Overload:

calculatePeakShapeMetrics(self, chromatogram: MSChromatogram, left: float, right: float, peak_height: float, peak_apex_pos: float) → PI_PeakShapeMetrics

Overload:

calculatePeakShapeMetrics(self, spectrum: MSSpectrum, left: float, right: float, peak_height: float, peak_apex_pos: float) → PI_PeakShapeMetrics

estimateBackground()#

Overload:

estimateBackground(self, chromatogram: MSChromatogram, left: float, right: float, peak_apex_pos: float) → PI_PeakBackground

Overload:

estimateBackground(self, spectrum: MSSpectrum, left: float, right: float, peak_apex_pos: float) → PI_PeakBackground

getDefaultParameters(self, in_0: Param) → None#

getDefaults(self) → Param#: Returns the default parameters

getName(self) → bytes | str | String#: Returns the name

getParameters(self) → Param#: Returns the parameters

getSubsections(self) → List[bytes]#

integratePeak()#

Overload:

integratePeak(self, chromatogram: MSChromatogram, left: float, right: float) → PI_PeakArea

Overload:

integratePeak(self, spectrum: MSSpectrum, left: float, right: float) → PI_PeakArea

setName(self, in_0: bytes | str | String) → None#: Sets the name

setParameters(self, param: Param) → None#: Sets the parameters