Class TestCasesHwe


  • public class TestCasesHwe
    extends java.lang.Object
    HWE test cases
    Author:
    pcingola
    • Field Summary

      Fields 
      Modifier and Type Field Description
      static boolean verbose  
    • Constructor Summary

      Constructors 
      Constructor Description
      TestCasesHwe()  
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void test_01()
      Calculate p-value using ChiSquare approximation
      void test_02()
      Calculate p-value using exact formula
      void test_02_table_1()
      Calculate "P[ n12 | n1, n2]" according to Table 1 in the paper "A Note on Exact test of Hardy Weinberg Equilibrium", G.
      void test_03_page_59()
      Calculate "P[ n12 | n1, n2]" according to Page 59 in the "Principles of population genetics"
      void test_04_pChi2_table_1()
      Calculate "P_{HWE}" using Chi-square approximation.
      void test_04_pHwe_table_1()
      Calculate "P_{HWE}" according to Table 1 in the paper "A Note on Exact test of Hardy Weinberg Equilibrium", G.
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    • Field Detail

      • verbose

        public static boolean verbose
    • Constructor Detail

      • TestCasesHwe

        public TestCasesHwe()
    • Method Detail

      • test_01

        public void test_01()
        Calculate p-value using ChiSquare approximation
      • test_02

        public void test_02()
        Calculate p-value using exact formula
      • test_02_table_1

        public void test_02_table_1()
        Calculate "P[ n12 | n1, n2]" according to Table 1 in the paper "A Note on Exact test of Hardy Weinberg Equilibrium", G. Abecasis et. al.
      • test_03_page_59

        public void test_03_page_59()
        Calculate "P[ n12 | n1, n2]" according to Page 59 in the "Principles of population genetics"
      • test_04_pChi2_table_1

        public void test_04_pChi2_table_1()
        Calculate "P_{HWE}" using Chi-square approximation. Compares results to Table 1 in the paper "A Note on Exact test of Hardy Weinberg Equilibrium", G. Abecasis et. al.
      • test_04_pHwe_table_1

        public void test_04_pHwe_table_1()
        Calculate "P_{HWE}" according to Table 1 in the paper "A Note on Exact test of Hardy Weinberg Equilibrium", G. Abecasis et. al.

        WARNING: The formula P_{HWE} in page 2 of the paper, seems to have two mistakes (probably typos?)