Package eu.isas.peptideshaker.scoring.targetdecoy

Class TargetDecoySeries

java.lang.Object
eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoySeries
public class TargetDecoySeries extends Object
This class will contain the PEP, FDR and FNR values of a target decoy map directly available for plotting.
Author:
Marc Vaudel

  • Constructor Details

    • TargetDecoySeries

      public TargetDecoySeries(HashMap<Double,TargetDecoyPoint> hitMap)
      Constructor.
      Parameters:
      hitMap - a map as present in target decoy maps

  • Method Details

    • getFDRResults

      public void getFDRResults(TargetDecoyResults targetDecoyResults)
      Completes the results at the desired FDR threshold.
      Parameters:
      targetDecoyResults - the results containing the threshold

    • getConfidenceResults

      public void getConfidenceResults(TargetDecoyResults targetDecoyResults)
      Completes the results at the desired confidence threshold.
      Parameters:
      targetDecoyResults - the results containing the threshold

    • getFNRResults

      public void getFNRResults(TargetDecoyResults targetDecoyResults)
      Completes the results at the desired FNR threshold.
      Parameters:
      targetDecoyResults - the results containing the threshold

    • getTdBins

      public double[] getTdBins()
      Returns the target decoy bins to use for the histogram.
      Returns:
      the target decoy bins to use for the histogram

    • getnTarget

      public double[] getnTarget()
      Returns the target series of the target decoy histogram.
      Returns:
      the target series of the target decoy histogram

    • getnDecoy

      public double[] getnDecoy()
      Returns the decoy series of the target decoy histogram.
      Returns:
      the decoy series of the target decoy histogram

    • getFDR

      public double[] getFDR()
      Returns the FDR series.
      Returns:
      the FDR series

    • getConfidence

      public double[] getConfidence()
      Returns the confidence series.
      Returns:
      the confidence series

    • getConfidenceLog

      public double[] getConfidenceLog()
      Returns the confidence log series.
      Returns:
      the confidence log series

    • getBenefit

      public double[] getBenefit()
      Returns the benefit series.
      Returns:
      the benefit series

    • getFNR

      public double[] getFNR()
      Returns the probabilistic FNR series.
      Returns:
      the probabilistic FNR series

    • getScores

      public double[] getScores()
      Returns the score series.
      Returns:
      the score series

    • getScoresLog

      public double[] getScoresLog()
      Returns the log score series.
      Returns:
      the log score series

    • getPEP

      public double[] getPEP()
      Returns the score series.
      Returns:
      the score series