com.compomics.util.experiment.identification
Class AScore
java.lang.Object
com.compomics.util.experiment.identification.AScore
public class AScore
- extends Object
This class scores PTM locations using the A-score.
- Author:
- Marc
Method Summary |
static HashMap<ArrayList<Integer>,Double> |
getAScore(Peptide peptide,
PTM ptm,
int nPTM,
MSnSpectrum spectrum,
ArrayList<PeptideFragmentIon.PeptideFragmentIonType> expectedFragmentIons,
HashMap<NeutralLoss,Integer> neutralLosses,
ArrayList<Integer> charges,
double mzTolerance)
Returns the A-score for the best PTM location. |
static HashMap<Integer,MSnSpectrum> |
getReducedSpectra(MSnSpectrum baseSpectrum,
double mzTolerance)
Generates a map containing the spectra filtered on intensity with a basis of 20*mz tolerance indexed by the depth used. |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
AScore
public AScore()
getAScore
public static HashMap<ArrayList<Integer>,Double> getAScore(Peptide peptide,
PTM ptm,
int nPTM,
MSnSpectrum spectrum,
ArrayList<PeptideFragmentIon.PeptideFragmentIonType> expectedFragmentIons,
HashMap<NeutralLoss,Integer> neutralLosses,
ArrayList<Integer> charges,
double mzTolerance)
- Returns the A-score for the best PTM location. In case the two best locations score the same they are both given with the score of 50.
- Parameters:
peptide
- The peptide of interestptm
- The name of the PTM to scorenPTM
- The number of occurrences where this PTM is expected on this peptidespectrum
- The corresponding spectrumexpectedFragmentIons
- The fragment ions to look forneutralLosses
- The neutral losses to look forcharges
- The fragment ions charges to look formzTolerance
- The m/z tolerance to use
- Returns:
- a map containing the best or two best PTM location(s) and the corresponding A-score
getReducedSpectra
public static HashMap<Integer,MSnSpectrum> getReducedSpectra(MSnSpectrum baseSpectrum,
double mzTolerance)
- Generates a map containing the spectra filtered on intensity with a basis of 20*mz tolerance indexed by the depth used. (see A-score paper for more details)
- Parameters:
baseSpectrum
- the base spectrummzTolerance
- the m/z tolerance
- Returns:
- a map containing the spectra filtered indexed by peak depth.
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