SequestLike (BioFSharp.Mz)

SequestLike Module

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

Functions and values

Function or value	Description
`autoCorrelation plusMinusMaxDelay vector` Full Usage: `autoCorrelation plusMinusMaxDelay vector` Parameters: plusMinusMaxDelay : `int` vector : `Vector<float>` Returns: `Vector<float>`	Computes the autocorrelation of the vector +/- plusMinusMaxDelay. plusMinusMaxDelay : `int` vector : `Vector<float>` Returns: `Vector<float>`
`calcSequestLikeScoresRevDecoy calcIonSeries massfunction (arg3, arg4) spectrum scanTime chargeState isolationWindowTargetMz possiblePeptideInfos spectrumID` Full Usage: `calcSequestLikeScoresRevDecoy calcIonSeries massfunction (arg3, arg4) spectrum scanTime chargeState isolationWindowTargetMz possiblePeptideInfos spectrumID` Parameters: calcIonSeries : `(Formula -> float) -> AminoAcid list -> PeakFamily<TaggedMass> list` massfunction : `Formula -> float` arg2 : `float` arg3 : `float` spectrum : `PeakArray<'a>` scanTime : `float` chargeState : `int` isolationWindowTargetMz : `float` possiblePeptideInfos : `LookUpResult<AminoAcid> list` spectrumID : `string` Returns: `SearchEngineResult<float> list`	Calculates the SequestLike Scores for all peptides (possiblePeptideInfos). calcIonSeries : `(Formula -> float) -> AminoAcid list -> PeakFamily<TaggedMass> list` massfunction : `Formula -> float` arg2 : `float` arg3 : `float` spectrum : `PeakArray<'a>` scanTime : `float` chargeState : `int` isolationWindowTargetMz : `float` possiblePeptideInfos : `LookUpResult<AminoAcid> list` spectrumID : `string` Returns: `SearchEngineResult<float> list`
`calcSequestScore (arg1, arg2) spectrum scanTime chargeState isolationWindowTargetMz theoreticalSpectra spectrumID` Full Usage: `calcSequestScore (arg1, arg2) spectrum scanTime chargeState isolationWindowTargetMz theoreticalSpectra spectrumID` Parameters: arg0 : `float` arg1 : `float` spectrum : `PeakArray<'a>` scanTime : `float` chargeState : `int` isolationWindowTargetMz : `float` theoreticalSpectra : `TheoreticalSpectrum<Vector<float>> list` spectrumID : `string` Returns: `SearchEngineResult<float> list`	Calculates the SequestLike Scores for all theoretical spectra. arg0 : `float` arg1 : `float` spectrum : `PeakArray<'a>` scanTime : `float` chargeState : `int` isolationWindowTargetMz : `float` theoreticalSpectra : `TheoreticalSpectrum<Vector<float>> list` spectrumID : `string` Returns: `SearchEngineResult<float> list`
`calcSequestScoreParallel (arg1, arg2) spectrum scanTime chargeState isolationWindowTargetMz theoreticalSpectra spectrumID` Full Usage: `calcSequestScoreParallel (arg1, arg2) spectrum scanTime chargeState isolationWindowTargetMz theoreticalSpectra spectrumID` Parameters: arg0 : `float` arg1 : `float` spectrum : `PeakArray<'a>` scanTime : `float` chargeState : `int` isolationWindowTargetMz : `float` theoreticalSpectra : `TheoreticalSpectrum<Vector<float>> list` spectrumID : `string` Returns: `SearchEngineResult<float> list`	Calculates the sequestLike Scores for all theoretical spectra. Implemented using Async parallel. arg0 : `float` arg1 : `float` spectrum : `PeakArray<'a>` scanTime : `float` chargeState : `int` isolationWindowTargetMz : `float` theoreticalSpectra : `TheoreticalSpectrum<Vector<float>> list` spectrumID : `string` Returns: `SearchEngineResult<float> list`
`calcXCorr p_nis ms_nis` Full Usage: `calcXCorr p_nis ms_nis` Parameters: p_nis : `Vector<float>` ms_nis : `Vector<float>` Returns: `float`	Calculates the Cross-Correlation of p_nis and ms_nis p_nis : `Vector<float>` ms_nis : `Vector<float>` Returns: `float`
`getTheoSpecs (arg1, arg2) chargeState possiblePeptideInfos` Full Usage: `getTheoSpecs (arg1, arg2) chargeState possiblePeptideInfos` Parameters: arg0 : `float` arg1 : `float` chargeState : `int` possiblePeptideInfos : `(LookUpResult<AminoAcid> * FragmentMasses) list` Returns: `TheoreticalSpectrum<Vector<float>> list`	Converts the fragment ion ladders to a theoretical Sequestlike spectrum at a given charge state. Subsequently, the spectrum is binned to the nearest mz bin (binwidth = 1 Da). Filters out peaks that are not within the scanLimits. arg0 : `float` arg1 : `float` chargeState : `int` possiblePeptideInfos : `(LookUpResult<AminoAcid> * FragmentMasses) list` Returns: `TheoreticalSpectrum<Vector<float>> list`
`predictIntensitySimpleModel ionType charge` Full Usage: `predictIntensitySimpleModel ionType charge` Parameters: ionType : `IonTypeFlag` charge : `float` Returns: `float`	Predicts the intensity of a theoretical peak based on the given charge and iontype. ionType : `IonTypeFlag` charge : `float` Returns: `float`
`predictOf (lowerScanLimit, upperScanLimit) charge ionSeries` Full Usage: `predictOf (lowerScanLimit, upperScanLimit) charge ionSeries` Parameters: lowerScanLimit : `float` upperScanLimit : `float` charge : `float` ionSeries : `PeakFamily<TaggedMass> list` Returns: `Vector<float>`	Converts the fragment ion ladder to a theoretical Sequestlike spectrum at a given charge state. Subsequently, the spectrum is binned to the nearest mz bin (binwidth = 1 Da). Filters out peaks that are not within the scanLimits. lowerScanLimit : `float` upperScanLimit : `float` charge : `float` ionSeries : `PeakFamily<TaggedMass> list` Returns: `Vector<float>`
`scoreSingle p_nis ms_nis` Full Usage: `scoreSingle p_nis ms_nis` Parameters: p_nis : `Vector<float>` ms_nis : `Vector<float>` Returns: `float`	Substracts Auto Correlation of measured normalized intensity spectrum (ms_nis). Subsequently, the Cross-Correlation of the predicted normalized intensity spectrum (p_nis) and ms_nis is calculated. p_nis : `Vector<float>` ms_nis : `Vector<float>` Returns: `float`
`setVectorInplace vector charge maxIndex lowerScanLimit taggedMass` Full Usage: `setVectorInplace vector charge maxIndex lowerScanLimit taggedMass` Parameters: vector : `Vector<float>` charge : `float` maxIndex : `int` lowerScanLimit : `int` taggedMass : `TaggedMass`	vector : `Vector<float>` charge : `float` maxIndex : `int` lowerScanLimit : `int` taggedMass : `TaggedMass`
`spectrumToIntensityArrayMinusAutoCorrelation (lowerScanLimit, upperScanLimit) spectrum` Full Usage: `spectrumToIntensityArrayMinusAutoCorrelation (lowerScanLimit, upperScanLimit) spectrum` Parameters: lowerScanLimit : `float` upperScanLimit : `float` spectrum : `PeakArray<'a>` Returns: `Vector<float>`	Measured spectrum to sequest-like normalized intensity array minus auto-correlation (delay 75 -> like in original sequest algorithm) ! Uses 10 as number of windows for window normalization (like in original sequest algorithm) lowerScanLimit : `float` upperScanLimit : `float` spectrum : `PeakArray<'a>` Returns: `Vector<float>`
`theoSpecOf (lowerScanLimit, upperScanLimit) maxcharge fragments` Full Usage: `theoSpecOf (lowerScanLimit, upperScanLimit) maxcharge fragments` Parameters: lowerScanLimit : `float` upperScanLimit : `float` maxcharge : `float` fragments : `PeakFamily<TaggedMass> list` Returns: `Vector<float>`	Converts the fragment ion ladder to a theoretical Sequestlike spectrum at a given charge state. lowerScanLimit : `float` upperScanLimit : `float` maxcharge : `float` fragments : `PeakFamily<TaggedMass> list` Returns: `Vector<float>`
`windowNormalizeIntensities intensities numberOfWindows` Full Usage: `windowNormalizeIntensities intensities numberOfWindows` Parameters: intensities : `Vector<float>` numberOfWindows : `int` Returns: `Vector<float>`	normalize the intensities within a window to maximum of the window Attention shortens the array (cuts) intensities : `Vector<float>` numberOfWindows : `int` Returns: `Vector<float>`