Package org.snpsift.testCases.unit
Class TestCasesHwe
- java.lang.Object
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- org.snpsift.testCases.unit.TestCasesHwe
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public class TestCasesHwe extends java.lang.Object
HWE test cases- Author:
- pcingola
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Field Summary
Fields Modifier and Type Field Description static boolean
verbose
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Constructor Summary
Constructors Constructor Description TestCasesHwe()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
test_01()
Calculate p-value using ChiSquare approximationvoid
test_02()
Calculate p-value using exact formulavoid
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.
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Method Detail
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test_01
public void test_01()
Calculate p-value using ChiSquare approximation
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test_02
public void test_02()
Calculate p-value using exact formula
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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.
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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"
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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.
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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?)
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