Package org.snpsift.testCases.unit
Class TestCasesHwe
java.lang.Object
org.snpsift.testCases.unit.TestCasesHwe
HWE test cases
- Author:
- pcingola
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Field Summary
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
test_01()
Calculate p-value using ChiSquare approximationvoid
test_02()
Calculate p-value using exact formulavoid
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.
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Field Details
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verbose
public static boolean verbose
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Constructor Details
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TestCasesHwe
public TestCasesHwe()
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Method Details
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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?)
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