ubic.erminej.analysis

Class AbstractGeneSetPvalGenerator

java.lang.Object

ubic.erminej.analysis.AbstractLongTask

ubic.erminej.analysis.AbstractGeneSetPvalGenerator

Direct Known Subclasses:

CorrelationPvalGenerator, GeneSetResamplingPvalGenerator, OraPvalGenerator, RocPvalGenerator

public abstract class AbstractGeneSetPvalGenerator
extends AbstractLongTask

Base implementation of pvalue generator

Version:

$Id: AbstractGeneSetPvalGenerator.java,v 1.20 2012/07/03 22:03:32 paul Exp $

Author:

Paul Pavlidis

Field Summary

Fields

Modifier and Type	Field and Description
protected static int	ALERT_UPDATE_FREQUENCY
protected GeneAnnotations	geneAnnots
protected Map<Gene,Double>	geneToScoreMap
protected StatusViewer	messenger
protected int	numGenesUsed
protected SettingsHolder	settings

Constructor Summary

Constructors

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

Method Summary

Methods

Modifier and Type	Method and Description
protected boolean	checkAspect(GeneSetTerm geneSetName, boolean missingAspectTreatedAsUsable)
protected boolean	checkAspectAndRedundancy(GeneSetTerm geneSetName) If GO data isn't initialized, this returns true.
abstract Map<GeneSetTerm,GeneSetResult>	generateGeneSetResults() Compute the results for all the gene sets under consideration.
int	getMaxClassSize()
StatusViewer	getMessenger()
int	getMinGeneSetSize()
int	getNumGenesUsed()
protected void	multipleTestCorrect(List<GeneSetTerm> sortedClasses, Map<GeneSetTerm,GeneSetResult> results) Perform multiple test correction during the multifunctionality correction.
int	numGenesInSet(GeneSetTerm t)
int	numProbesInSet(GeneSetTerm t)
protected List<Double>	ranksOfGenesInSet(Collection<Gene> genesInSet)
void	set_class_max_size(int value)
void	set_class_min_size(int value)

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

Field Detail

ALERT_UPDATE_FREQUENCY

protected static final int ALERT_UPDATE_FREQUENCY

See Also:

Constant Field Values

messenger

protected StatusViewer messenger

settings

protected SettingsHolder settings

geneToScoreMap

protected Map<Gene,Double> geneToScoreMap

geneAnnots

protected GeneAnnotations geneAnnots

numGenesUsed

protected int numGenesUsed

Constructor Detail

AbstractGeneSetPvalGenerator

public AbstractGeneSetPvalGenerator(SettingsHolder set,
                            GeneAnnotations annots,
                            Map<Gene,Double> geneToScoreMap,
                            StatusViewer messenger)

Parameters:

set -

annots -

geneToScoreMap - can be null if the method doesn't use gene scores; must already be log-transformed, if requested.

messenger2 -

Method Detail

generateGeneSetResults

public abstract Map<GeneSetTerm,GeneSetResult> generateGeneSetResults()

Compute the results for all the gene sets under consideration.

Returns:

A map of GeneSetTerm to GeneSetResult.

getMaxClassSize

public int getMaxClassSize()

getMessenger

public StatusViewer getMessenger()

getMinGeneSetSize

public int getMinGeneSetSize()

Returns:

getNumGenesUsed

public int getNumGenesUsed()

numGenesInSet

public int numGenesInSet(GeneSetTerm t)

numProbesInSet

public int numProbesInSet(GeneSetTerm t)

set_class_max_size

public void set_class_max_size(int value)

Parameters:

value -

set_class_min_size

public void set_class_min_size(int value)

Parameters:

value -

checkAspect

protected boolean checkAspect(GeneSetTerm geneSetName,
                  boolean missingAspectTreatedAsUsable)

Parameters:

geneSetName -

missingAspectTreatedAsUsable - Whether gene sets missing an aspect should be treated as usable or not. This parameter is provided partly for testing. Global setting can override this if set to true.

Returns:

true if the set should be retained (e.g. it is in the correct aspect )

checkAspectAndRedundancy

protected boolean checkAspectAndRedundancy(GeneSetTerm geneSetName)

If GO data isn't initialized, this returns true. If there is no aspect associated with the gene set, return false.

Parameters:

geneSetName -

Returns:

multipleTestCorrect

protected void multipleTestCorrect(List<GeneSetTerm> sortedClasses,
                       Map<GeneSetTerm,GeneSetResult> results)

Perform multiple test correction during the multifunctionality correction. DOES NOT SUPPORT WESTFALL-YOUNG CORRECTION

Parameters:

sortedClasses -

results -

ranksOfGenesInSet

protected List<Double> ranksOfGenesInSet(Collection<Gene> genesInSet)

Parameters:

genesInSet -

Returns:

1-based ranks of genes in the set, taking into account "bigger is better" and log-transformation.