ubic.erminej.analysis

Class ExperimentScoreQuickPvalGenerator

java.lang.Object

ubic.erminej.analysis.AbstractLongTask

ubic.erminej.analysis.AbstractGeneSetPvalGenerator

ubic.erminej.analysis.GeneSetResamplingPvalGenerator

ubic.erminej.analysis.ExperimentScoreQuickPvalGenerator

public class ExperimentScoreQuickPvalGenerator
extends GeneSetResamplingPvalGenerator

Does the same thing as GeneSetResamplingPvalGeneratorbut is stripped-down for using during resampling.

Version:

$Id: ExperimentScoreQuickPvalGenerator.java,v 1.11 2012/03/02 20:15:45 paul Exp $

Author:

Paul Pavlidis

Field Summary

Fields inherited from class ubic.erminej.analysis.GeneSetResamplingPvalGenerator

generator, hist

Fields inherited from class ubic.erminej.analysis.AbstractGeneSetPvalGenerator

ALERT_UPDATE_FREQUENCY, geneAnnots, geneToScoreMap, messenger, numGenesUsed, settings

Constructor Summary

Constructors

Constructor and Description
ExperimentScoreQuickPvalGenerator(SettingsHolder settings, GeneAnnotations a, Map<Gene,Double> geneToScoreMap, StatusViewer messenger)

Method Summary

Methods

Modifier and Type	Method and Description
double	classPvalue(GeneSetTerm geneSetName) This is stripped-down version of classPvalue.

Methods inherited from class ubic.erminej.analysis.GeneSetResamplingPvalGenerator

classPval, classPvalGeneratorRaw, generateGeneSetResults, generateGeneSetResults, scoreToPval

Methods inherited from class ubic.erminej.analysis.AbstractGeneSetPvalGenerator

checkAspect, checkAspectAndRedundancy, getMaxClassSize, getMessenger, getMinGeneSetSize, getNumGenesUsed, multipleTestCorrect, numGenesInSet, numProbesInSet, ranksOfGenesInSet, set_class_max_size, set_class_min_size

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

ExperimentScoreQuickPvalGenerator

public ExperimentScoreQuickPvalGenerator(SettingsHolder settings,
                                 GeneAnnotations a,
                                 Map<Gene,Double> geneToScoreMap,
                                 StatusViewer messenger)

Method Detail

classPvalue

public double classPvalue(GeneSetTerm geneSetName)

This is stripped-down version of classPvalue. We use this when doing permutations, it is much faster.

Parameters:

class_name - String

group_pval_map - Map

probesToPvals - Map

Returns:

double

Throws:

IllegalStateException