Class TestCasesHwe

java.lang.Object
org.snpsift.testCases.unit.TestCasesHwe

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

    Fields
    Modifier and Type
    Field
    Description
    static boolean
     
  • Constructor Summary

    Constructors
    Constructor
    Description
     
  • Method Summary

    Modifier and Type
    Method
    Description
    void
    Calculate p-value using ChiSquare approximation
    void
    Calculate p-value using exact formula
    void
    Calculate "P[ n12 | n1, n2]" according to Table 1 in the paper "A Note on Exact test of Hardy Weinberg Equilibrium", G.
    void
    Calculate "P[ n12 | n1, n2]" according to Page 59 in the "Principles of population genetics"
    void
    Calculate "P_{HWE}" using Chi-square approximation.
    void
    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 Details

    • verbose

      public static boolean verbose
  • Constructor Details

    • TestCasesHwe

      public TestCasesHwe()
  • Method Details

    • 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?)