ChargeState (BioFSharp.Mz)

ChargeState Module

Namespace: BioFSharp.Mz
Assembly: BioFSharp.Mz.dll

Types

Type	Description
AssignedCharge
ChargeDetermParams
PutativeIsotopeCluster

Functions and values

Function or value	Description
`createAssignedCharge precSpecID productSpecId precMZ charge putMass mZChargeDev score distanceRealTheoPeakSpacing subSetLength startPeakIntensity peaks positionMetricPValue` Full Usage: `createAssignedCharge precSpecID productSpecId precMZ charge putMass mZChargeDev score distanceRealTheoPeakSpacing subSetLength startPeakIntensity peaks positionMetricPValue` Parameters: precSpecID : `string` productSpecId : `string` precMZ : `float` charge : `int` putMass : `float` mZChargeDev : `float` score : `float` distanceRealTheoPeakSpacing : `float list` subSetLength : `int` startPeakIntensity : `float` peaks : `Set<Peak>` positionMetricPValue : `float option` Returns: `AssignedCharge`	precSpecID : `string` productSpecId : `string` precMZ : `float` charge : `int` putMass : `float` mZChargeDev : `float` score : `float` distanceRealTheoPeakSpacing : `float list` subSetLength : `int` startPeakIntensity : `float` peaks : `Set<Peak>` positionMetricPValue : `float option` Returns: `AssignedCharge`
`createChargeDetermParams expectedMinimalCharge expectedMaximumCharge width minIntensity deltaMinIntensity nrOfRndSpectra` Full Usage: `createChargeDetermParams expectedMinimalCharge expectedMaximumCharge width minIntensity deltaMinIntensity nrOfRndSpectra` Parameters: expectedMinimalCharge : `int` expectedMaximumCharge : `int` width : `float` minIntensity : `float` deltaMinIntensity : `float` nrOfRndSpectra : `int` Returns: `ChargeDetermParams`	expectedMinimalCharge : `int` expectedMaximumCharge : `int` width : `float` minIntensity : `float` deltaMinIntensity : `float` nrOfRndSpectra : `int` Returns: `ChargeDetermParams`
`createPutativeIsotopeCluster peaks sourceSetLength subSetLength` Full Usage: `createPutativeIsotopeCluster peaks sourceSetLength subSetLength` Parameters: peaks : `PeakList<Peak>` sourceSetLength : `int` subSetLength : `int` Returns: `PutativeIsotopeCluster`	peaks : `PeakList<Peak>` sourceSetLength : `int` subSetLength : `int` Returns: `PutativeIsotopeCluster`
`empiricalPValueOfSim initGenerateMzSpecDevWithMemF (nrOfPeaksInSubSet, charge) score` Full Usage: `empiricalPValueOfSim initGenerateMzSpecDevWithMemF (nrOfPeaksInSubSet, charge) score` Parameters: initGenerateMzSpecDevWithMemF : `int * 'a -> 'b array` nrOfPeaksInSubSet : `int` charge : `'a` score : `'b` Returns: `float`	stdv 0.01516580549 Returns the empirically determined PValue. The PValue is the quotient of simulated mzChargeDeviations lower than the mzChargeDeviation observed divided by their total number initGenerateMzSpecDevWithMemF : `int * 'a -> 'b array` nrOfPeaksInSubSet : `int` charge : `'a` score : `'b` Returns: `float`
`empiricalRightPValueOf distribution score` Full Usage: `empiricalRightPValueOf distribution score` Parameters: distribution : `'a array` score : `'a` Returns: `float`	Returns the empirically determined PValue. The PValue is the quotient of simulated mzChargeDeviations lower than the mzChargeDeviation observed divided by their total number distribution : `'a array` score : `'a` Returns: `float`
`getChargeBy chargeDeterminationParams meanOfInterPeakDistances` Full Usage: `getChargeBy chargeDeterminationParams meanOfInterPeakDistances` Parameters: chargeDeterminationParams : `ChargeDetermParams` meanOfInterPeakDistances : `float` Returns: `int`	Returns a charge state based on a given meanOfInterPeakDistances. The list of possible charge states is defined by the user. chargeDeterminationParams : `ChargeDetermParams` meanOfInterPeakDistances : `float` Returns: `int`
`getRelPeakPosInWindowBy mzData intensityData width minIntensity deltaMinIntensity startIdx` Full Usage: `getRelPeakPosInWindowBy mzData intensityData width minIntensity deltaMinIntensity startIdx` Parameters: mzData : `float[]` intensityData : `float[]` width : `float` minIntensity : `float` deltaMinIntensity : `float` startIdx : `int` Returns: `float * PutativeIsotopeCluster`	Returns a Collection of MZIntensityPeaks, The Collection starts with the first Element on the right side of the startIdx. and ends either with the last element of the mzIntensityArray or when the MzDistance to the highest Peak exceeds the given windowwidth. mzData : `float[]` intensityData : `float[]` width : `float` minIntensity : `float` deltaMinIntensity : `float` startIdx : `int` Returns: `float * PutativeIsotopeCluster`
`getScore elementsInSubSet elementsInSourceSet deviationPeakDistanceToTheoDistance` Full Usage: `getScore elementsInSubSet elementsInSourceSet deviationPeakDistanceToTheoDistance` Parameters: elementsInSubSet : `int` elementsInSourceSet : `int` deviationPeakDistanceToTheoDistance : `float` Returns: `float`	Returns a empirically determined Score to achieve a Ranking of SubSets. The optimal weighting of the parameters was determined via Linear Discriminant Analysis. elementsInSubSet : `int` elementsInSourceSet : `int` deviationPeakDistanceToTheoDistance : `float` Returns: `float`
`initMzDevOfRndSpec rnd chargeStateDetermParams peakPosStdDev` Full Usage: `initMzDevOfRndSpec rnd chargeStateDetermParams peakPosStdDev` Parameters: rnd : `Random` chargeStateDetermParams : `ChargeDetermParams` peakPosStdDev : `float` Returns: `int * float -> float array`	Returns Function to generate random spectra and to calculate their mzChargeDeviations. rnd : `Random` chargeStateDetermParams : `ChargeDetermParams` peakPosStdDev : `float` Returns: `int * float -> float array`
`interPeakDistanceBy stdDev assignedCharge` Full Usage: `interPeakDistanceBy stdDev assignedCharge` Parameters: stdDev : `float` assignedCharge : `float` Returns: `float`	Returns a possible InterPeakDistance by a given charge state. The retrieved distance follows a normaldistribution centered around the theoretical interPeakDistance. The standardDeviation is dependent on the used mass spectrometer stdDev : `float` assignedCharge : `float` Returns: `float`
`kullbackLeiblerDivergenceOf qTo p` Full Usage: `kullbackLeiblerDivergenceOf qTo p` Parameters: qTo : `float[]` p : `float[]` Returns: `float option`	qTo : `float[]` p : `float[]` Returns: `float option`
`mzChargeDeviationBy interPeakDistances theoreticalInterIsotopeDistance` Full Usage: `mzChargeDeviationBy interPeakDistances theoreticalInterIsotopeDistance` Parameters: interPeakDistances : `float seq` theoreticalInterIsotopeDistance : `float` Returns: `float`	Returns the MZChargeDeviation based on the theoreticalInterIsotopeDistance as a Measure for central tendency at a given ChargeState. interPeakDistances : `float seq` theoreticalInterIsotopeDistance : `float` Returns: `float`
`mzDevOfRndSpec rnd chargeStateDetermParams peakPosStdDev (chainLength, charge)` Full Usage: `mzDevOfRndSpec rnd chargeStateDetermParams peakPosStdDev (chainLength, charge)` Parameters: rnd : `Random` chargeStateDetermParams : `ChargeDetermParams` peakPosStdDev : `float` chainLength : `int` charge : `float` Returns: `float array`	Creates a user defined amount of random spectra of defined length. Returns the mzChargeDeviation of each simulated Spectrum rnd : `Random` chargeStateDetermParams : `ChargeDetermParams` peakPosStdDev : `float` chainLength : `int` charge : `float` Returns: `float array`
`mzDistancesOf mzIntensityPeaks` Full Usage: `mzDistancesOf mzIntensityPeaks` Parameters: mzIntensityPeaks : `PeakList<'a>` Returns: `float list`	Calculates the mzDistances of a List of MzIntensityPeaks mzIntensityPeaks : `PeakList<'a>` Returns: `float list`
`n14MassToLambda mass` Full Usage: `n14MassToLambda mass` Parameters: mass : `float` Returns: `float`	mass : `float` Returns: `float`
`n15MassToLambda mass` Full Usage: `n15MassToLambda mass` Parameters: mass : `float` Returns: `float`	mass : `float` Returns: `float`
`normalizePeaksByIntensitySum peaks` Full Usage: `normalizePeaksByIntensitySum peaks` Parameters: peaks : `Set<Peak>` Returns: `float array`	peaks : `Set<Peak>` Returns: `float array`
`peakPosStdDevBy putativeChargeStates` Full Usage: `peakPosStdDevBy putativeChargeStates` Parameters: putativeChargeStates : `AssignedCharge list` Returns: `float`	Returns the StandardDeviation of the PeakDistances putativeChargeStates : `AssignedCharge list` Returns: `float`
`poissonEstofMassTrunc massToLambda limit mass` Full Usage: `poissonEstofMassTrunc massToLambda limit mass` Parameters: massToLambda : `float -> float` limit : `int` mass : `float` Returns: `float array`	massToLambda : `float -> float` limit : `int` mass : `float` Returns: `float array`
`poissonProb lambda xValue` Full Usage: `poissonProb lambda xValue` Parameters: lambda : `float` xValue : `float` Returns: `float`	lambda : `float` xValue : `float` Returns: `float`
`powerSetOf putCluster` Full Usage: `powerSetOf putCluster` Parameters: putCluster : `PutativeIsotopeCluster` Returns: `PutativeIsotopeCluster list`	Creates the PowerSet of a given Collection of MZIntensityPeaks. Adds a StartPeak with the relative Position 0 and the relative Intensity 1 to each subSet. putCluster : `PutativeIsotopeCluster` Returns: `PutativeIsotopeCluster list`
`putativePrecursorChargeStatesBy chargeDeterminationParams mzData intensityData precursorSpecID productSpecID precursorMZ` Full Usage: `putativePrecursorChargeStatesBy chargeDeterminationParams mzData intensityData precursorSpecID productSpecID precursorMZ` Parameters: chargeDeterminationParams : `ChargeDetermParams` mzData : `float[]` intensityData : `float[]` precursorSpecID : `string` productSpecID : `string` precursorMZ : `float` Returns: `AssignedCharge list`	Returns list of putative precursorChargeStates along with Properties used for evaluation. chargeDeterminationParams : `ChargeDetermParams` mzData : `float[]` intensityData : `float[]` precursorSpecID : `string` productSpecID : `string` precursorMZ : `float` Returns: `AssignedCharge list`
`removeSubSetsOfBestHit assignedCharges` Full Usage: `removeSubSetsOfBestHit assignedCharges` Parameters: assignedCharges : `AssignedCharge list` Returns: `AssignedCharge list`	Returns a List of tested AssignedCharges. assignedCharges : `AssignedCharge list` Returns: `AssignedCharge list`
`rndIntBetween rnd lowerBorder upperBorder` Full Usage: `rndIntBetween rnd lowerBorder upperBorder` Parameters: rnd : `Random` lowerBorder : `int` upperBorder : `int` Returns: `int`	Returns a random integer between a lower and a upper Value rnd : `Random` lowerBorder : `int` upperBorder : `int` Returns: `int`
`rndMzIntensityEntityCollectionBy rnd maxCount stdDev maxCharge maxDistance minChainLength` Full Usage: `rndMzIntensityEntityCollectionBy rnd maxCount stdDev maxCharge maxDistance minChainLength` Parameters: rnd : `Random` maxCount : `int` stdDev : `float` maxCharge : `int` maxDistance : `float` minChainLength : `int` Returns: `PutativeIsotopeCluster option`	Creates a random MzIntensityEntityCollection rnd : `Random` maxCount : `int` stdDev : `float` maxCharge : `int` maxDistance : `float` minChainLength : `int` Returns: `PutativeIsotopeCluster option`