Package ubic.basecode.math

Class Wilcoxon

java.lang.Object

ubic.basecode.math.Wilcoxon

public class Wilcoxon
extends Object

Implements methods from supplementary file I of "Comparing functional annotation analyses with Catmap", Thomas Breslin, Patrik Ed�n and Morten Krogh, BMC Bioinformatics 2004, 5:193 doi:10.1186/1471-2105-5-193

Note that in the Catmap code, zero-based ranks are used, but these are converted to one-based before computation of pvalues. Therefore this code uses one-based ranks throughout.

Version:

Id

Author:

pavlidis

See Also:

ROC

Constructor Summary

Constructors

Constructor	Description
Wilcoxon()

Method Summary

Modifier and Type	Method	Description
static double	exactWilcoxonP(double[] a, double[] b)	Convenience method that computes a p-value using input of two double arrays.
static double	exactWilcoxonP(int N, int n, int R)
static double	wilcoxonP(int N, int n, long R)	Only use when you know there are no ties.
static double	wilcoxonP(int N, int n, long R, boolean ties)
static double	wilcoxonP(int N, List<Double> ranks)

Methods inherited from class java.lang.Object

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

Constructor Detail

Wilcoxon

public Wilcoxon()

Method Detail

exactWilcoxonP

public static double exactWilcoxonP(double[] a,
                                    double[] b)

Convenience method that computes a p-value using input of two double arrays. They must not contain missing values or ties.

exactWilcoxonP

public static double exactWilcoxonP(int N,
                                    int n,
                                    int R)

wilcoxonP

public static double wilcoxonP(int N,
                               int n,
                               long R)

Only use when you know there are no ties.

wilcoxonP

public static double wilcoxonP(int N,
                               int n,
                               long R,
                               boolean ties)

Parameters:

N - number of all Items

n - number of class Items

R - rankSum for items in the class. (one-based)

ties - set to true if you know there are ties

wilcoxonP

public static double wilcoxonP(int N,
                               List<Double> ranks)

Parameters:

N - total number of items (in and not in the class)

ranks - of items in the class (one-based)