org.expasy.mzjava.stats.statscores

Class FitDecoyScoreStatistics

java.lang.Object

org.expasy.mzjava.stats.statscores.ScoreStatistics

org.expasy.mzjava.stats.statscores.FitDecoyScoreStatistics

public class FitDecoyScoreStatistics
extends ScoreStatistics

This method is appropriate if for separate decoy and target searches and if more than one hit is considered. The decoy distribution is fitted into the target distribution using linear regression.

Version:

0.0

Author:

Markus Muller

Nested Class Summary

Nested classes/interfaces inherited from class org.expasy.mzjava.stats.statscores.ScoreStatistics

ScoreStatistics.SortAction

Field Summary

Fields

Modifier and Type	Field and Description
protected float	targetDecoyRatio

Fields inherited from class org.expasy.mzjava.stats.statscores.ScoreStatistics

decoyScores, fdrValues, qValues, targetScores

Constructor Summary

Constructors

Constructor and Description
FitDecoyScoreStatistics(double[] targetScores, double[] decoyScores)
FitDecoyScoreStatistics(double[] targetScores, double[] decoyScores, ScoreStatistics.SortAction sortAction)
FitDecoyScoreStatistics(float[] targetScores, float[] decoyScores)
FitDecoyScoreStatistics(float[] targetScores, float[] decoyScores, ScoreStatistics.SortAction sortAction)
FitDecoyScoreStatistics(gnu.trove.list.TDoubleList targetScores, gnu.trove.list.TDoubleList decoyScores)
FitDecoyScoreStatistics(gnu.trove.list.TDoubleList targetScores, gnu.trove.list.TDoubleList decoyScores, ScoreStatistics.SortAction sortAction)
FitDecoyScoreStatistics(gnu.trove.list.TFloatList targetScores, gnu.trove.list.TFloatList decoyScores)
FitDecoyScoreStatistics(gnu.trove.list.TFloatList targetScores, gnu.trove.list.TFloatList decoyScores, ScoreStatistics.SortAction sortAction)

Method Summary

Methods

Modifier and Type	Method and Description
protected void	calculateFDR()
float	getTargetDecoyRatio()

Methods inherited from class org.expasy.mzjava.stats.statscores.ScoreStatistics

calculateQValue, getDecoyScores, getNrDecoyScores, getNrTargetScores, getQValue, getScoreForQValue, getTargetScores

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

targetDecoyRatio

protected float targetDecoyRatio

Constructor Detail

FitDecoyScoreStatistics

public FitDecoyScoreStatistics(float[] targetScores,
                       float[] decoyScores)

FitDecoyScoreStatistics

public FitDecoyScoreStatistics(float[] targetScores,
                       float[] decoyScores,
                       ScoreStatistics.SortAction sortAction)

FitDecoyScoreStatistics

public FitDecoyScoreStatistics(double[] targetScores,
                       double[] decoyScores)

FitDecoyScoreStatistics

public FitDecoyScoreStatistics(double[] targetScores,
                       double[] decoyScores,
                       ScoreStatistics.SortAction sortAction)

FitDecoyScoreStatistics

public FitDecoyScoreStatistics(gnu.trove.list.TFloatList targetScores,
                       gnu.trove.list.TFloatList decoyScores)

FitDecoyScoreStatistics

public FitDecoyScoreStatistics(gnu.trove.list.TFloatList targetScores,
                       gnu.trove.list.TFloatList decoyScores,
                       ScoreStatistics.SortAction sortAction)

FitDecoyScoreStatistics

public FitDecoyScoreStatistics(gnu.trove.list.TDoubleList targetScores,
                       gnu.trove.list.TDoubleList decoyScores)

FitDecoyScoreStatistics

public FitDecoyScoreStatistics(gnu.trove.list.TDoubleList targetScores,
                       gnu.trove.list.TDoubleList decoyScores,
                       ScoreStatistics.SortAction sortAction)

Method Detail

getTargetDecoyRatio

public float getTargetDecoyRatio()

calculateFDR

protected void calculateFDR()

Specified by:

calculateFDR in class ScoreStatistics