org.expasy.mzjava.stats.statscores

Class FirstRankScoreStatistics

java.lang.Object

org.expasy.mzjava.stats.statscores.ScoreStatistics

org.expasy.mzjava.stats.statscores.FirstRankScoreStatistics

public class FirstRankScoreStatistics
extends ScoreStatistics

This class calculates FDRs and qValues for searches where each spectrum matches only one - either target or decoy - entry. False matches to the target entries must have equal probability as matches to decoy entries. This is for example approximately the case when using concatenated target decoy databases of the same size.

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

decoyScores, fdrValues, qValues, targetScores

Constructor Summary

Constructors

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

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

Constructor Detail

FirstRankScoreStatistics

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

FirstRankScoreStatistics

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

FirstRankScoreStatistics

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

FirstRankScoreStatistics

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

FirstRankScoreStatistics

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

FirstRankScoreStatistics

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

FirstRankScoreStatistics

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

FirstRankScoreStatistics

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

Method Detail

calculateFDR

protected void calculateFDR()

Specified by:

calculateFDR in class ScoreStatistics