ubic.erminej.analysis

Class ResamplingCorrelationGeneSetScore

java.lang.Object

ubic.erminej.analysis.AbstractLongTask

ubic.erminej.analysis.AbstractResamplingGeneSetScore

ubic.erminej.analysis.ResamplingCorrelationGeneSetScore

All Implemented Interfaces:

NullDistributionGenerator

public class ResamplingCorrelationGeneSetScore
extends AbstractResamplingGeneSetScore

Version:

$Id: ResamplingCorrelationGeneSetScore.java,v 1.6 2012/05/27 02:54:30 paul Exp $

Author:

pavlidis

Field Summary

Fields inherited from class ubic.erminej.analysis.AbstractResamplingGeneSetScore

classMaxSize, classMinSize, hist, histogramMax, histogramMin, log, NORMAL_APPROX_SAMPLE_FREQUENCY, numClasses, numRuns, SPEDUPSIZEEXTRASTEP, SPEEDUPSIZECUT, TOLERANCE, useNormalApprox, useSpeedUp

Constructor Summary

Constructors

Constructor and Description
ResamplingCorrelationGeneSetScore(SettingsHolder settings, DoubleMatrix<Probe,String> dataMatrix)

Method Summary

Methods

Modifier and Type	Method and Description
Histogram	generateNullDistribution(StatusViewer messenger) Build background distributions of within-gene set mean correlations.
Histogram	generateNulldistribution(StatusViewer m, long randomSeed) Generate a null distribution, using a selected random seed.
double	geneSetMeanCorrel(int[] indicesToSelect) Compute the average correlation for a set of vectors.
void	setRandomSeed(long randomSeed)

Methods inherited from class ubic.erminej.analysis.AbstractResamplingGeneSetScore

getHist, setClassMaxSize, setUseNormalApprox, setUseSpeedUp

Methods inherited from class ubic.erminej.analysis.AbstractLongTask

ifInterruptedStop

Methods inherited from class java.lang.Object

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

Constructor Detail

ResamplingCorrelationGeneSetScore

public ResamplingCorrelationGeneSetScore(SettingsHolder settings,
                                 DoubleMatrix<Probe,String> dataMatrix)

Parameters:

dataMatrix -

Method Detail

generateNulldistribution

public Histogram generateNulldistribution(StatusViewer m,
                                 long randomSeed)

Generate a null distribution, using a selected random seed.

Parameters:

m -

randomSeed -

Returns:

generateNullDistribution

public Histogram generateNullDistribution(StatusViewer messenger)

Build background distributions of within-gene set mean correlations. This requires computing a lot of correlations.

Returns:

histogram containing the random distributions of correlations.

geneSetMeanCorrel

public double geneSetMeanCorrel(int[] indicesToSelect)

Compute the average correlation for a set of vectors.

Parameters:

indicesToSelect - - rows of the matrix that will get compared.

Returns:

mean correlation within the matrix.

setRandomSeed

public void setRandomSeed(long randomSeed)