Package org.gorpipe.gor.util

Class GChiSquared2by2

java.lang.Object
org.gorpipe.gor.util.GChiSquared2by2
public class GChiSquared2by2
extends java.lang.Object
Chi-squared for 2-by-2 contingency tables.

  • Method Summary

    Modifier and Type Method Description
    static double computeLogLikelihoodChiSquared​(int o11, int o12, int o21, int o22)
    Compute the likelihood ratio chi-squared value for the 2-by-2 table [o11 o12] [o21 o22].
    static double computePearsonChiSquared​(int o11, int o12, int o21, int o22)
    Compute the Pearson's chi-squared value for the 2-by-2 table [o11 o12] [o21 o22].
    static double getChiSqValue​(double pvalue)
    Get the chi-squared value corresponding to a p-value (assuming 1 degree of freedom).
    static double getFiniteChiSqValue​(double pvalue, int o11, int o12, int o21, int o22)
    Get the chi-squared value corresponding to a p-value (assuming 1 degree of freedom), but if the p-value is zero compute the chi-squared value directly from the table.
    static double getPValue​(double chisq)
    Get the p-value from a chi-squared value for a 2-by-2 table.

    Methods inherited from class java.lang.Object

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

  • Method Details

    • computePearsonChiSquared

      public static double computePearsonChiSquared​(int o11, int o12, int o21, int o22)
      Compute the Pearson's chi-squared value for the 2-by-2 table [o11 o12] [o21 o22].
      Parameters:
      o11 - entry (1,1)
      o12 - entry (1,2)
      o21 - entry (2,1)
      o22 - entry (2,2)
      Returns:
      the chi squared value

    • computeLogLikelihoodChiSquared

      public static double computeLogLikelihoodChiSquared​(int o11, int o12, int o21, int o22)
      Compute the likelihood ratio chi-squared value for the 2-by-2 table [o11 o12] [o21 o22].
      Parameters:
      o11 - entry (1,1)
      o12 - entry (1,2)
      o21 - entry (2,1)
      o22 - entry (2,2)
      Returns:
      the chi squared value

    • getPValue

      public static double getPValue​(double chisq)
      Get the p-value from a chi-squared value for a 2-by-2 table. That is, get the p-value for a chi-squared distribution with 1 degree of freedom.
      Parameters:
      chisq - the chi-squared value
      Returns:
      the p-value

    • getChiSqValue

      public static double getChiSqValue​(double pvalue)
      Get the chi-squared value corresponding to a p-value (assuming 1 degree of freedom).
      Parameters:
      pvalue - the p-value
      Returns:
      the chi-squared value

    • getFiniteChiSqValue

      public static double getFiniteChiSqValue​(double pvalue, int o11, int o12, int o21, int o22)
      Get the chi-squared value corresponding to a p-value (assuming 1 degree of freedom), but if the p-value is zero compute the chi-squared value directly from the table. This is preferable to returning an infinite value, if the chi-squared values are used for correcting the p-values (genomic control).
      Parameters:
      pvalue - the p-value
      o11 - entry (1,1)
      o12 - entry (1,2)
      o21 - entry (2,1)
      o22 - entry (2,2)
      Returns:
      the chi-squared value