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Re-enabling disabled test. Apparently T-tests are very picky about your using an unbiased variance. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5622 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2011-04-13 03:05:50 +00:00
parent 42bc003f46
commit efe6c539ac
2 changed files with 8 additions and 8 deletions
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4
java/src/org/broadinstitute/sting/utils/MathUtils.java
View File

@ -88,8 +88,8 @@ public class MathUtils {
double mn = mean.doubleValue();
double var = 0;
for ( Number n : numbers ) { var += ( ! ignoreNan || ! Double.isNaN(n.doubleValue())) ? (n.doubleValue()-mn)*(n.doubleValue()-mn) : 0; }
if ( ignoreNan ) { return var/nonNanSize(numbers); }
return var/numbers.size();
if ( ignoreNan ) { return var/(nonNanSize(numbers)-1); }
return var/(numbers.size()-1);
}
public static double variance(Collection<Number> numbers, Number mean) {

12
java/test/org/broadinstitute/sting/oneoffprojects/walkers/RegionalAssociationUnitTest.java
View File

@ -27,26 +27,26 @@ public class RegionalAssociationUnitTest extends BaseTest {
@BeforeClass
public void init() { }
//@Test
@Test
private void testTStatistics() {
logger.warn("Testing T statistics");
TTest test1 = new TTest();
test1.setCaseData((Collection) Arrays.asList(1,1,2,3,4));
test1.setControlData((Collection) Arrays.asList(10, 10, 20, 30, 40));
Assert.assertEquals(AssociationTestRunner.getTestValues(test1).second.first,0.1702,1e-2);
Assert.assertEquals(AssociationTestRunner.getTestValues(test1).second.first,0.02697891,1e-8);
TTest test2 = new TTest();
test2.setCaseData((Collection) Arrays.asList(5, 6, 5, 2, 3, 8, 7, 12, 10, 6, 4, 2, 8, 7, 3));
test2.setControlData((Collection) Arrays.asList(1, 6, 7, 2, 3, 3, 4, 1, 2, 5, 7, 3, 10, 3, 3, 2, 3));
Assert.assertEquals(AssociationTestRunner.getTestValues(test2).second.first, 0.5805, 1e-2);
Assert.assertEquals(AssociationTestRunner.getTestValues(test2).second.first, 0.04100948, 1e-8);
TTest test3 = new TTest();
test3.setCaseData((Collection) Arrays.asList(94,25,68,4,27,51,9,10,91,61,61,37,39,44,36,27,86,33,3,38,5,6,28,93,30,56,81,8,40,44));
test3.setControlData((Collection) Arrays.asList(6,64,96,85,20,74,93,18,31,20,88,38,80,50,33,81,35,8,2,69,49,6,26,74,79,63,63,96,45,18));
Assert.assertEquals(AssociationTestRunner.getTestValues(test3).second.first,0.8229,1e-4);
Assert.assertEquals(AssociationTestRunner.getTestValues(test3).second.first,0.2309763,1e-7);
TTest test4 = new TTest();
test4.setCaseData((Collection) Arrays.asList(14,8,8,17,8,12,10,10,13,9,13,9,9,12,12,11,16,12,13,16,10,13,11,16,13,16,11,13,9,16,16,14,9,14,17,10,15,15,9,15,17,15,17,12,10,13,11,14,8,14));
test4.setControlData((Collection) Arrays.asList(7,1,4,2,3,7,8,5,5,4,10,6,4,9,2,9,9,3,3,10,1,8,9,5,3,7,2,7,10,9,4,9,2,10,10,3,2,3,4,4,5,10,9,4,3,5,6,10,5,10));
Assert.assertEquals(AssociationTestRunner.getTestValues(test4).second.first,0.1006,1e-4);
Assert.assertEquals(AssociationTestRunner.getTestValues(test4).first,1.657989,1e-6);
Assert.assertEquals(AssociationTestRunner.getTestValues(test4).second.first,4.291725e-20,1e-19);
Assert.assertEquals(AssociationTestRunner.getTestValues(test4).first,11.60592,1e-5);
}
@Test