Class TestCasesFisherExactTest
java.lang.Object
org.snpeff.snpEffect.testCases.unity.TestCasesFisherExactTest
Test for Hypergeometric distribution and Fisher exact test
- Author:
- pcingola
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Field Summary
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Constructor Summary
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Method Summary
Modifier and TypeMethodDescriptionvoid
Create commands in R to run and get test resultsvoid
test_0()
void
void
void
void
Compare Fisher exact test to Chi^2 approximation
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Field Details
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MAX_DIFF
public static double MAX_DIFF
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Constructor Details
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TestCasesFisherExactTest
public TestCasesFisherExactTest()
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Method Details
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generate_test
public void generate_test()Create commands in R to run and get test results -
test_0
@Test public void test_0() -
test_03_fisher
@Test public void test_03_fisher() -
test_04_fisher
@Test public void test_04_fisher() -
test_05_fisher
@Test public void test_05_fisher() -
test_06_fisher_vs_chi2
@Test public void test_06_fisher_vs_chi2()Compare Fisher exact test to Chi^2 approximationFrom R: > data <- matrix(c(25, 5, 15, 15), ncol=2, byrow=T) > data [,1] [,2] [1,] 25 5 [2,] 15 15
> chisq.test(data,correct=FALSE)
Pearson's Chi-squared test
data: data X-squared = 7.5, df = 1, p-value = 0.00617
> fisher.test(data, alternative="greater")
Fisher's Exact Test for Count Data
data: data p-value = 0.006349 alternative hypothesis: true odds ratio is greater than 1 95 percent confidence interval: 1.587561 Inf sample estimates: odds ratio 4.859427
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