Package gorsat.process

Class StatisticalAdjustment

  • public class StatisticalAdjustment
extends java.lang.Object

    • Method Summary

      All Methods Static Methods Concrete Methods 
      Modifier and Type Method Description
      static void benjamini_hochberg​(double[] pValues, double[] bh)
      Runs a Benjamini Hochberg correction on an ordered vector of p values.
      static void benjamini_yekutieli​(double[] pValues, double[] by)
      Runs a Benjamini-Yekutieli correction on an ordered vector of p values.
      static double bonferroni​(double pValue, int len)  
      static double genomic_control_correct_p​(double pValue, double invSqrtLambda)  
      static double genomic_control_correct_z​(double z, double invSqrtLambda)
      The genomic control corrected chi-2 statistic is computed by dividing the initial chi-2 statistic by lambda (the genomic inflation estimate).
      static double getInvSqrtLambda_p​(double[] p)
      Returns 1 / sqrt(lambda) where lambda is the genomic inflation estimate.
      static void holm_bonferroni​(double[] pValues, double[] holm)
      Runs a Holm-Bonferroni correction on an ordered vector of p values.
      static void invert​(int[] perm)
      Inverts a permutation.
      static void sidak_sd​(double[] pValues, double[] sidak)
      Runs a Sidak step down correction on an ordered vector of p values.
      static double sidak_ss​(double pValue, int len)  

      • Methods inherited from class java.lang.Object

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

    • Method Detail

      • genomic_control_correct_z

        public static double genomic_control_correct_z​(double z,
                                               double invSqrtLambda)
        The genomic control corrected chi-2 statistic is computed by dividing the initial chi-2 statistic by lambda (the genomic inflation estimate). If we have a z statistic > 0, then the corresponding the chi statistic is z^2. The correctied chi-statistic is z^2 / lambda so the corrected p-value is P(CHI_2(1) > z^2/lambda) = P(N(0,1) > z / sqrt(lambda) or N(0,1) < -z / sqrt(lambda)) = 2 * P(N(0,1) < -z / sqrt(lambda)) Which explains the formulas in the next two methods.

      • genomic_control_correct_p

        public static double genomic_control_correct_p​(double pValue,
                                               double invSqrtLambda)

      • getInvSqrtLambda_p

        public static double getInvSqrtLambda_p​(double[] p)
        Returns 1 / sqrt(lambda) where lambda is the genomic inflation estimate. The genomic inflation estimate is computed by taking the median of the chi stats (with 1 df) from which the p values are computed and dividing it by chi_inv_half. Let C be a CHI_2(1) random variable and N a N(0,1) random variable. Then C ~ N^2 so P(C > x^2) = P(N > |x| or N < -|x|) = 2 * P(N < -|x|). Thus, we can compute the chi-stats from the p values by normalInverse(p / 2)^2.

      • bonferroni

        public static double bonferroni​(double pValue,
                                int len)

      • holm_bonferroni

        public static void holm_bonferroni​(double[] pValues,
                                   double[] holm)
        Runs a Holm-Bonferroni correction on an ordered vector of p values.

      • sidak_ss

        public static double sidak_ss​(double pValue,
                              int len)

      • sidak_sd

        public static void sidak_sd​(double[] pValues,
                            double[] sidak)
        Runs a Sidak step down correction on an ordered vector of p values.

      • benjamini_hochberg

        public static void benjamini_hochberg​(double[] pValues,
                                      double[] bh)
        Runs a Benjamini Hochberg correction on an ordered vector of p values.

      • benjamini_yekutieli

        public static void benjamini_yekutieli​(double[] pValues,
                                       double[] by)
        Runs a Benjamini-Yekutieli correction on an ordered vector of p values.

      • invert

        public static void invert​(int[] perm)
        Inverts a permutation.