Kernel_MassTrace#

class pyopenms.Kernel_MassTrace#

Bases: object

Cython implementation of _Kernel_MassTrace

Original C++ documentation is available here

__init__()#

Overload:

__init__(self) → None

Overload:

__init__(self, in_0: Kernel_MassTrace) → None

Overload:

__init__(self, trace_peaks: List[Peak2D]) → None

Methods

`__init__`	Overload:
`computeFwhmArea`(self)
`computeFwhmAreaSmooth`(self)	Computes chromatographic peak area within the FWHM range.
`computePeakArea`(self)	Sums intensities of all peaks in the mass trace
`computeSmoothedPeakArea`(self)	Sums all non-negative (smoothed!) intensities in the mass trace
`estimateFWHM`(self, in_0)	Estimates FWHM of chromatographic peak in seconds (based on either raw or smoothed intensities)
`findMaxByIntPeak`(self, in_0)	Returns the index of the mass trace's highest peak within the MassTrace container (based either on raw or smoothed intensities)
`getAverageMS1CycleTime`(self)	Returns average scan time of mass trace
`getCentroidMZ`(self)	Returns the centroid m/z
`getCentroidRT`(self)	Returns the centroid RT
`getCentroidSD`(self)	Returns the centroid SD
`getConvexhull`(self)	Returns the mass trace's convex hull
`getFWHM`(self)	Returns FWHM
`getFWHMborders`(self)	Returns FWHM boarders
`getIntensity`(self, in_0)	Returns the intensity
`getLabel`(self)	Returns label of mass trace
`getMaxIntensity`(self, in_0)	Returns the max intensity
`getQuantMethod`(self)	Check if area or median is used for quantification
`getSize`(self)	Returns the number of peaks contained in the mass trace
`getSmoothedIntensities`(self)	Returns smoothed intensities (empty if no smoothing was explicitly done beforehand!)
`getTraceLength`(self)	Returns the length of the trace (as difference in RT)
`setCentroidSD`(self, tmp_sd)
`setLabel`(self, label)	Sets label of mass trace
`setQuantMethod`(self, method)	Determine if area or median is used for quantification
`setSmoothedIntensities`(self, db_vec)	Sets smoothed intensities (smoothing is done externally, e.g.
`updateMeanMZ`(self)	Compute & update centroid m/z as mean of m/z values
`updateMedianMZ`(self)	Compute & update centroid m/z as median of m/z values
`updateMedianRT`(self)	Compute & update centroid RT as median position of intensities
`updateSmoothedMaxRT`(self)
`updateSmoothedWeightedMeanRT`(self)
`updateWeightedMZsd`(self)	Compute & update m/z standard deviation of mass trace as weighted mean of m/z values
`updateWeightedMeanMZ`(self)	Compute & update centroid m/z as weighted mean of m/z values
`updateWeightedMeanRT`(self)	Compute & update centroid RT as a intensity-weighted mean of RTs

Attributes

fwhm_mz_avg

computeFwhmArea(self) → float#

computeFwhmAreaSmooth(self) → float#: Computes chromatographic peak area within the FWHM range.

computePeakArea(self) → float#: Sums intensities of all peaks in the mass trace

computeSmoothedPeakArea(self) → float#: Sums all non-negative (smoothed!) intensities in the mass trace

estimateFWHM(self, in_0: bool) → int#: Estimates FWHM of chromatographic peak in seconds (based on either raw or smoothed intensities)

findMaxByIntPeak(self, in_0: bool) → int#: Returns the index of the mass trace’s highest peak within the MassTrace container (based either on raw or smoothed intensities)

fwhm_mz_avg#

getAverageMS1CycleTime(self) → float#: Returns average scan time of mass trace

getCentroidMZ(self) → float#: Returns the centroid m/z

getCentroidRT(self) → float#: Returns the centroid RT

getCentroidSD(self) → float#: Returns the centroid SD

getConvexhull(self) → ConvexHull2D#: Returns the mass trace’s convex hull

getFWHM(self) → float#: Returns FWHM

getFWHMborders(self) → List[int, int]#: Returns FWHM boarders

getIntensity(self, in_0: bool) → float#: Returns the intensity

getLabel(self) → bytes | str | String#: Returns label of mass trace

getMaxIntensity(self, in_0: bool) → float#: Returns the max intensity

getQuantMethod(self) → int#: Check if area or median is used for quantification

getSize(self) → int#: Returns the number of peaks contained in the mass trace

getSmoothedIntensities(self) → List[float]#: Returns smoothed intensities (empty if no smoothing was explicitly done beforehand!)

getTraceLength(self) → float#: Returns the length of the trace (as difference in RT)

setCentroidSD(self, tmp_sd: float) → None#

setLabel(self, label: bytes | str | String) → None#: Sets label of mass trace

setQuantMethod(self, method: int) → None#: Determine if area or median is used for quantification

setSmoothedIntensities(self, db_vec: List[float]) → None#: Sets smoothed intensities (smoothing is done externally, e.g. by LowessSmoothing)

updateMeanMZ(self) → None#: Compute & update centroid m/z as mean of m/z values

updateMedianMZ(self) → None#: Compute & update centroid m/z as median of m/z values

updateMedianRT(self) → None#: Compute & update centroid RT as median position of intensities

updateSmoothedMaxRT(self) → None#

updateSmoothedWeightedMeanRT(self) → None#

updateWeightedMZsd(self) → None#

Compute & update m/z standard deviation of mass trace as weighted mean of m/z values

Make sure to call update(Weighted)(Mean|Median)MZ() first! <br> use getCentroidSD() to get result

updateWeightedMeanMZ(self) → None#: Compute & update centroid m/z as weighted mean of m/z values

updateWeightedMeanRT(self) → None#: Compute & update centroid RT as a intensity-weighted mean of RTs