ubic.erminej.analysis

Class RocPvalGenerator

java.lang.Object

ubic.erminej.analysis.AbstractLongTask

ubic.erminej.analysis.AbstractGeneSetPvalGenerator

ubic.erminej.analysis.RocPvalGenerator

public class RocPvalGenerator
extends AbstractGeneSetPvalGenerator

Compute gene set p values based on the receiver operating characteristic (ROC).

Version:

$Id: RocPvalGenerator.java,v 1.23 2013/04/29 16:55:38 paul Exp $

Author:

Paul Pavlidis

Field Summary

Fields inherited from class ubic.erminej.analysis.AbstractGeneSetPvalGenerator

ALERT_UPDATE_FREQUENCY, geneAnnots, geneToScoreMap, messenger, numGenesUsed, settings

Constructor Summary

Constructors

Constructor and Description
RocPvalGenerator(SettingsHolder set, GeneAnnotations an, Map<Gene,Double> geneToScoreMap, StatusViewer messenger)

Method Summary

Methods

Modifier and Type	Method and Description
Map<GeneSetTerm,GeneSetResult>	generateGeneSetResults() Compute the results for all the gene sets under consideration.
protected Map<GeneSetTerm,GeneSetResult>	generateGeneSetResults(boolean useMultifunctionalityCorrection)

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

RocPvalGenerator

public RocPvalGenerator(SettingsHolder set,
                GeneAnnotations an,
                Map<Gene,Double> geneToScoreMap,
                StatusViewer messenger)

Method Detail

generateGeneSetResults

public Map<GeneSetTerm,GeneSetResult> generateGeneSetResults()

Description copied from class: AbstractGeneSetPvalGenerator

Compute the results for all the gene sets under consideration.

Specified by:

generateGeneSetResults in class AbstractGeneSetPvalGenerator

Returns:

A map of GeneSetTerm to GeneSetResult.

generateGeneSetResults

protected Map<GeneSetTerm,GeneSetResult> generateGeneSetResults(boolean useMultifunctionalityCorrection)

Parameters:

useMultifunctionalityCorrection -

Returns: