PeakGroup#

class pyopenms.PeakGroup#

Bases: object

Cython implementation of _PeakGroup

Original C++ documentation is available here

Class describing a deconvolved mass. A mass contains multiple (LogMz) peaks of different charges and isotope indices. PeakGroup is the set of such peaks representing a single monoisotopic mass.

__init__()#

Overload:

__init__(self) → None

Overload:

__init__(self, in_0: PeakGroup) → None

Overload:

__init__(self, min_abs_charge: int, max_abs_charge: int, is_positive: bool) → None

Methods

`__init__`
`empty`(self)	Returns true if no peaks
`getAvgDaError`(self)	Returns average Da error
`getAvgPPMError`(self)	Returns average ppm error
`getChargeIntensity`(self, abs_charge)	Returns intensity for given charge
`getChargeIsotopeCosine`(self, abs_charge)	Returns isotope cosine for given charge
`getChargeSNR`(self, abs_charge)	Returns SNR for given charge
`getChargeScore`(self)	Returns the charge fit score
`getFeatureIndex`(self)	Returns the feature index
`getIndex`(self)	Returns the peak group index
`getIntensity`(self)	Returns the summed intensity
`getIsotopeCosine`(self)	Returns the isotope cosine score
`getIsotopeDaDistance`(self)	Returns distance between consecutive isotopes
`getIsotopeIntensities`(self)	Returns per-isotope intensities
`getMassErrors`(self, ppm)	Returns mass errors per isotope
`getMinNegativeIsotopeIndex`(self)	Returns minimum negative isotope index
`getMonoMass`(self)	Returns the monoisotopic mass
`getPeakOccupancy`(self)	Returns peak occupancy (0-1)
`getQscore`(self)	Returns the quality score (0-1)
`getQscore2D`(self)	Returns the 2D quality score incorporating feature-level information
`getQvalue`(self)	Returns the q-value for FDR
`getRepAbsCharge`(self)	Returns the representative charge
`getSNR`(self)	Returns the signal-to-noise ratio
`getScanNumber`(self)	Returns the scan number
`getTargetDecoyType`(self)	Returns target/decoy type
`isPositive`(self)	Returns true if positive ionization mode
`isTargeted`(self)	Returns true if this peak group was targeted
`push_back`(self, pg)	Adds a LogMzPeak
`reserve`(self, n)	Reserves space for n peaks
`setAvgPPMError`(self, error)	Sets average ppm error
`setChargeIsotopeCosine`(self, abs_charge, cos)	Sets isotope cosine for given charge
`setChargeSNR`(self, abs_charge, c_snr)	Sets SNR for given charge
`setChargeScore`(self, charge_score)	Sets the charge fit score
`setFeatureIndex`(self, findex)	Sets the feature index
`setIndex`(self, i)	Sets the peak group index
`setIsotopeCosine`(self, cos)	Sets the isotope cosine score
`setIsotopeDaDistance`(self, d)	Sets isotope distance
`setMonoisotopicMass`(self, mono_mass)	Sets the monoisotopic mass
`setQscore`(self, qscore)	Sets the quality score
`setQscore2D`(self, fqscore)	Sets the 2D quality score
`setQvalue`(self, q)	Sets the q-value
`setRepAbsCharge`(self, max_snr_abs_charge)	Sets the representative charge
`setSNR`(self, snr)	Sets the SNR
`setScanNumber`(self, scan_number)	Sets the scan number
`setTargetDecoyType`(self, index)	Sets the target/decoy type
`setTargeted`(self)	Marks this peak group as targeted
`size`(self)	Returns number of LogMzPeaks
`sort`(self)	Sorts peaks by log m/z

TargetDecoyType#: alias of __TargetDecoyType

empty(self) → bool#: Returns true if no peaks

getAvgDaError(self) → float#: Returns average Da error

getAvgPPMError(self) → float#: Returns average ppm error

getChargeIntensity(self, abs_charge: int) → float#: Returns intensity for given charge

getChargeIsotopeCosine(self, abs_charge: int) → float#: Returns isotope cosine for given charge

getChargeSNR(self, abs_charge: int) → float#: Returns SNR for given charge

getChargeScore(self) → float#: Returns the charge fit score

getFeatureIndex(self) → int#: Returns the feature index

getIndex(self) → int#: Returns the peak group index

getIntensity(self) → float#: Returns the summed intensity

getIsotopeCosine(self) → float#: Returns the isotope cosine score

getIsotopeDaDistance(self) → float#: Returns distance between consecutive isotopes

getIsotopeIntensities(self) → List[float]#: Returns per-isotope intensities

getMassErrors(self, ppm: bool) → List[float]#: Returns mass errors per isotope

getMinNegativeIsotopeIndex(self) → int#: Returns minimum negative isotope index

getMonoMass(self) → float#: Returns the monoisotopic mass

getPeakOccupancy(self) → float#: Returns peak occupancy (0-1)

getQscore(self) → float#: Returns the quality score (0-1)

getQscore2D(self) → float#: Returns the 2D quality score incorporating feature-level information

getQvalue(self) → float#: Returns the q-value for FDR

getRepAbsCharge(self) → int#: Returns the representative charge

getSNR(self) → float#: Returns the signal-to-noise ratio

getScanNumber(self) → int#: Returns the scan number

getTargetDecoyType(self) → int#: Returns target/decoy type

isPositive(self) → bool#: Returns true if positive ionization mode

isTargeted(self) → bool#: Returns true if this peak group was targeted

push_back(self, pg: LogMzPeak) → None#: Adds a LogMzPeak

reserve(self, n: int) → None#: Reserves space for n peaks

setAvgPPMError(self, error: float) → None#: Sets average ppm error

setChargeIsotopeCosine(self, abs_charge: int, cos: float) → None#: Sets isotope cosine for given charge

setChargeSNR(self, abs_charge: int, c_snr: float) → None#: Sets SNR for given charge

setChargeScore(self, charge_score: float) → None#: Sets the charge fit score

setFeatureIndex(self, findex: int) → None#: Sets the feature index

setIndex(self, i: int) → None#: Sets the peak group index

setIsotopeCosine(self, cos: float) → None#: Sets the isotope cosine score

setIsotopeDaDistance(self, d: float) → None#: Sets isotope distance

setMonoisotopicMass(self, mono_mass: float) → None#: Sets the monoisotopic mass

setQscore(self, qscore: float) → None#: Sets the quality score

setQscore2D(self, fqscore: float) → None#: Sets the 2D quality score

setQvalue(self, q: float) → None#: Sets the q-value

setRepAbsCharge(self, max_snr_abs_charge: int) → None#: Sets the representative charge

setSNR(self, snr: float) → None#: Sets the SNR

setScanNumber(self, scan_number: int) → None#: Sets the scan number

setTargetDecoyType(self, index: int) → None#: Sets the target/decoy type

setTargeted(self) → None#: Marks this peak group as targeted

size(self) → int#: Returns number of LogMzPeaks

sort(self) → None#: Sorts peaks by log m/z