Package org.snpeff.gsa

Class ScoreList

java.lang.Object
org.snpeff.gsa.ScoreList
Direct Known Subclasses:
PvaluesList
public class ScoreList extends Object
A list of scores
Author:
pcingola

  • Nested Class Summary

    Nested Classes
    Modifier and Type
    Class
    Description
    static enum 
    ScoreList.ScoreSummary
     

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    static final double
    SIGNIFICANCE_LEVEL_95
     

  • Constructor Summary

    Constructors
    Constructor
    Description
    ScoreList()
     

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    add(double score)
    Add a p-value to the list
    double
    avg()
    Get average
    double
    avgLargestTop(int topN)
    Get average pvalue (largest N)
    double
    avgSmallestTop(int topN)
    Get average score (smallest N)
    double
    cdf(double p)
    Cumulative distribution function of p-values: P[ pValues <= p ] (i.e.
    double
    cdfUpper(double p)
    Cumulative distribution function of p-values: P[ pValues > p ] (i.e.
    static double
    chiSquareCDFComplementary(double chiSquare, int nu)
    Upper tail 1 - ChiSquareCDF(p)
    protected double
    getDefaultValue()
     
    String
    getGeneId()
     
    double
    getScore(int index)
     
    double
    max()
    Get minimum pvalue
    double
    min()
    Get minimum pvalue
    double
    pValueBonferroni()
    Minimum p-value corrected using Bonferroni
    double
    pValueFdr(double alpha)
    Combine p-values using FDR procedure References: http://en.wikipedia.org/wiki/False_discovery_rate
    double
    pValueFisherChi2()
    Combine p-values using Fisher's method References: http://en.wikipedia.org/wiki/Fisher's_method
    double
    pValueSimes()
    Combine p-values using Simes's procedure References: http://biomet.oxfordjournals.org/content/73/3/751
    double
    pValueZScore()
    Combine p-values using Stouffer's Z-score method References: http://en.wikipedia.org/wiki/Fisher's_method (scroll down to Stouffer's method)
    double
    quantile(double quantile)
    Get pvalue quantile
    double
    score(ScoreList.ScoreSummary pvalueSummary)
    Create a single pValue representing the gene
    void
    setGeneId(String geneId)
     
    int
    size()
     
    double
    sum()
    Get sum of scores
    String
    toString()
     

    Methods inherited from class java.lang.Object

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

  • Field Details

    • SIGNIFICANCE_LEVEL_95

      public static final double SIGNIFICANCE_LEVEL_95
      See Also:

  • Constructor Details

    • ScoreList

      public ScoreList()

  • Method Details

    • chiSquareCDFComplementary

      public static double chiSquareCDFComplementary(double chiSquare, int nu)
      Upper tail 1 - ChiSquareCDF(p)
      Parameters:
      chiSquare -
      nu -
      Returns:

    • add

      public void add(double score)
      Add a p-value to the list
      Parameters:
      score -

    • avg

      public double avg()
      Get average
      Returns:

    • avgLargestTop

      public double avgLargestTop(int topN)
      Get average pvalue (largest N)
      Returns:

    • avgSmallestTop

      public double avgSmallestTop(int topN)
      Get average score (smallest N)
      Returns:

    • cdf

      public double cdf(double p)
      Cumulative distribution function of p-values: P[ pValues <= p ] (i.e. lower tail).
      Parameters:
      p -
      Returns:

    • cdfUpper

      public double cdfUpper(double p)
      Cumulative distribution function of p-values: P[ pValues > p ] (i.e. upper tail).
      Parameters:
      p -
      Returns:

    • getDefaultValue

      protected double getDefaultValue()

    • getGeneId

      public String getGeneId()

    • getScore

      public double getScore(int index)

    • max

      public double max()
      Get minimum pvalue
      Returns:

    • min

      public double min()
      Get minimum pvalue
      Returns:

    • pValueBonferroni

      public double pValueBonferroni()
      Minimum p-value corrected using Bonferroni
      Returns:

    • pValueFdr

      public double pValueFdr(double alpha)
      Combine p-values using FDR procedure References: http://en.wikipedia.org/wiki/False_discovery_rate
      Returns:
      A combined p-value

    • pValueFisherChi2

      public double pValueFisherChi2()
      Combine p-values using Fisher's method References: http://en.wikipedia.org/wiki/Fisher's_method
      Returns:

    • pValueSimes

      public double pValueSimes()
      Combine p-values using Simes's procedure References: http://biomet.oxfordjournals.org/content/73/3/751
      Returns:
      A combined p-value

    • pValueZScore

      public double pValueZScore()
      Combine p-values using Stouffer's Z-score method References: http://en.wikipedia.org/wiki/Fisher's_method (scroll down to Stouffer's method)
      Returns:
      A combined p-value

    • quantile

      public double quantile(double quantile)
      Get pvalue quantile
      Returns:

    • score

      public double score(ScoreList.ScoreSummary pvalueSummary)
      Create a single pValue representing the gene
      Returns:

    • setGeneId

      public void setGeneId(String geneId)

    • size

      public int size()

    • sum

      public double sum()
      Get sum of scores
      Returns:

    • toString

      public String toString()
      Overrides:
      toString in class Object