TestCasesGenePvalueList (SnpEff 5.1 API)

java.lang.Object
- org.snpeff.snpEffect.testCases.unity.TestCasesGenePvalueList

public class TestCasesGenePvalueList
extends java.lang.Object

GenePvalueList statistics test case

Author:: pcingola

Field Summary

Fields
Modifier and Type Field Description

static double EPSILON

Constructor Summary

Constructors
Constructor Description

TestCasesGenePvalueList()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`test_01()`	Combined p-value : MIN
`void`	`test_02()`	Combined p-value : AVG
`void`	`test_03()`	Combined p-value : AVG10
`void`	`test_04()`	Complementary CDF for Chi^2 distribution
`void`	`test_05()`	Combined p-value : FISHER_CHI_SQUARE
`void`	`test_06()`	Combined p-value : Z_SCORES
`void`	`test_07()`	Combined p-value : FDR
`void`	`test_08()`	Test quantile
`void`	`test_09()`	Test CDF (cumulative distribution function)

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - EPSILON
```
public static final double EPSILON
```
    See Also:
    
    Constant Field Values
- Constructor Detail
  - TestCasesGenePvalueList
```
public TestCasesGenePvalueList()
```
- Method Detail
  - test_01
```
@Test
public void test_01()
```
    Combined p-value : MIN
  - test_02
```
@Test
public void test_02()
```
    Combined p-value : AVG
  - test_03
```
@Test
public void test_03()
```
    Combined p-value : AVG10
  - test_04
```
@Test
public void test_04()
```
    Complementary CDF for Chi^2 distribution
  - test_05
```
@Test
public void test_05()
```
    Combined p-value : FISHER_CHI_SQUARE
  - test_06
```
@Test
public void test_06()
```
    Combined p-value : Z_SCORES
  - test_07
```
@Test
public void test_07()
```
    Combined p-value : FDR
    Reference for this test: http://stat.ethz.ch/R-manual/R-devel/library/stats/html/p.adjust.html
    R code: set.seed(123) x <- rnorm(50, mean = c(rep(0, 25), rep(3, 25))) p <- 2*pnorm(sort(-abs(x))) p.adjust(p, "fdr")
  - test_08
```
@Test
public void test_08()
```
    Test quantile
  - test_09
```
@Test
public void test_09()
```
    Test CDF (cumulative distribution function)