Package org.snpeff.probablility

Class Hypergeometric

java.lang.Object

org.snpeff.probablility.Hypergeometric

public class Hypergeometric
extends java.lang.Object

Calculate hypergeometric distribution using an optimized algorithm that avoids problems with big factorials. Also calculated Fisher's exact test In general everything is expressed in a 2x2 'contingency' table form sequence of 'n' draws from a finite population without replacement drawn not drawn | total defective k D - k | D nondefective n - k N + k - n - D | N - D ----------------------------+---------- total n N - n | N This can be viewed as if we have a bag of N marbles having D white marbles, and we take a sample of n marbles(without replacement) N : Total marbles D : White marbles => N-D : Black marbles n : marbles drawn => N-n : not drawn k : white marbles drawn

Author:

pcingola

Field Summary

Fields

Modifier and Type	Field	Description
static double	EPSILON	A small number

Method Summary

Modifier and Type	Method	Description
boolean	checkHypergeometricParams(int k, int N, int D, int n)	Check if hypergeometric paramters are correct
static Hypergeometric	get()
double	hypergeometric(int k, int N, int D, int n)	See http://en.wikipedia.org/wiki/Hypergeometric_distribution
static void	main(java.lang.String[] args)
java.lang.String	toR(int k, int N, int D, int n)	Convert values to 'R' command

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

EPSILON

public static double EPSILON

A small number

Method Detail

get

public static Hypergeometric get()

main

public static void main(java.lang.String[] args)

checkHypergeometricParams

public boolean checkHypergeometricParams(int k,
                                         int N,
                                         int D,
                                         int n)

Check if hypergeometric paramters are correct

Parameters:

k -

N -

D -

n -

Returns:

hypergeometric

public double hypergeometric(int k,
                             int N,
                             int D,
                             int n)

See http://en.wikipedia.org/wiki/Hypergeometric_distribution

Parameters:

k - : white marbles drawn

N - : Total marbles

D - : White marbles => N-D : Black marbles

n - : marbles drawn => N-n : not drawn

Returns:

Hypergeometric distribution References: http://en.wikipedia.org/wiki/Fisher%27s_exact_test http://en.wikipedia.org/wiki/Hypergeometric_distribution

toR

public java.lang.String toR(int k,
                            int N,
                            int D,
                            int n)

Convert values to 'R' command

Returns: