baseCode - 0.2.5

Clover coverage report - baseCode - 0.2.5

Coverage timestamp: Tue Apr 12 2005 11:31:58 EDT

FRAMES NO FRAMES

file stats:	LOC:	60		Methods:	2
	NCLOC:	23		Classes:	1

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MultipleTestCorrection.java

 package baseCode.math;
 
 import cern.colt.list.DoubleArrayList;
 
 /**
  * Methods for p-value correction of sets of hypothesis tests.
  * <p>
  * Copyright (c) 2004
  * </p>
  * <p>
  * Institution:: Columbia University
  * </p>
  * 
  * @author Paul Pavlidis
  * @version $Id: MultipleTestCorrection.java,v 1.6 2004/07/27 03:18:57 pavlidis Exp $
  */
 public class MultipleTestCorrection {
 
    /**
     * Determine the Bonferroni pvalue threshold to maintain the family wise error rate (assuming pvalues are
     * independent).
     * 
     * @param pvalues The pvalues
     * @param fwe The family wise error rate
     * @return The minimum pvalue that maintains the FWE
     */
    public static double BonferroniCut( DoubleArrayList pvalues, double fwe ) {
       int numpvals = pvalues.size();
       return fwe / numpvals;
    }
 
    /**
     * Benjamini-Hochberg method. Determines the maximum p value to maintain the false discovery rate. (Assuming pvalues
     * are independent);
     * 
     * @param pvalues list of pvalues. Need not be sorted.
     * @param fdr false discovery rate
     * @return The maximum pvalue that maintains the false discovery rate
     */
    public static double BenjaminiHochbergCut( DoubleArrayList pvalues,
          double fdr ) {
       int numpvals = pvalues.size();
       DoubleArrayList pvalcop = pvalues.copy();
       pvalcop.sort();
       pvalcop.reverse();
 
       int n = pvalcop.size();
       double thresh = fdr * n / numpvals;
 
       for ( int i = 0; i < n; i++ ) {
          double p = pvalcop.get( i );
 
          if ( p < thresh ) {
             return p;
          }
       }
       return 0.0;
    }
 
 }

1		package baseCode.math;
2
3		import cern.colt.list.DoubleArrayList;
4
5		/**
6		* Methods for p-value correction of sets of hypothesis tests.
7		* <p>
8		* Copyright (c) 2004
9		* </p>
10		* <p>
11		* Institution:: Columbia University
12		* </p>
13		*
14		* @author Paul Pavlidis
15		* @version $Id: MultipleTestCorrection.java,v 1.6 2004/07/27 03:18:57 pavlidis Exp $
16		*/
17		public class MultipleTestCorrection {
18
19		/**
20		* Determine the Bonferroni pvalue threshold to maintain the family wise error rate (assuming pvalues are
21		* independent).
22		*
23		* @param pvalues The pvalues
24		* @param fwe The family wise error rate
25		* @return The minimum pvalue that maintains the FWE
26		*/
27	0	public static double BonferroniCut( DoubleArrayList pvalues, double fwe ) {
28	0	int numpvals = pvalues.size();
29	0	return fwe / numpvals;
30		}
31
32		/**
33		* Benjamini-Hochberg method. Determines the maximum p value to maintain the false discovery rate. (Assuming pvalues
34		* are independent);
35		*
36		* @param pvalues list of pvalues. Need not be sorted.
37		* @param fdr false discovery rate
38		* @return The maximum pvalue that maintains the false discovery rate
39		*/
40	0	public static double BenjaminiHochbergCut( DoubleArrayList pvalues,
41		double fdr ) {
42	0	int numpvals = pvalues.size();
43	0	DoubleArrayList pvalcop = pvalues.copy();
44	0	pvalcop.sort();
45	0	pvalcop.reverse();
46
47	0	int n = pvalcop.size();
48	0	double thresh = fdr * n / numpvals;
49
50	0	for ( int i = 0; i < n; i++ ) {
51	0	double p = pvalcop.get( i );
52
53	0	if ( p < thresh ) {
54	0	return p;
55		}
56		}
57	0	return 0.0;
58		}
59
60		}