Class TestCasesFisherExactTest

java.lang.Object
org.snpeff.snpEffect.testCases.unity.TestCasesFisherExactTest

public class TestCasesFisherExactTest extends Object
Test for Hypergeometric distribution and Fisher exact test
Author:
pcingola
  • Field Details

    • MAX_DIFF

      public static double MAX_DIFF
  • Constructor Details

    • TestCasesFisherExactTest

      public TestCasesFisherExactTest()
  • Method Details

    • 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 approximation

      From 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