ubic.erminej.analysis

Class OraPvalGenerator

java.lang.Object

ubic.erminej.analysis.AbstractLongTask

ubic.erminej.analysis.AbstractGeneSetPvalGenerator

ubic.erminej.analysis.OraPvalGenerator

public class OraPvalGenerator
extends AbstractGeneSetPvalGenerator

Compute gene set scores based on over-representation analysis (ORA).

Version:

$Id: OraPvalGenerator.java,v 1.39 2013/05/18 20:23:03 paul Exp $

Author:

Paul Pavlidis

Field Summary

Fields

Modifier and Type	Field and Description
protected double	geneScoreThreshold

Fields inherited from class ubic.erminej.analysis.AbstractGeneSetPvalGenerator

ALERT_UPDATE_FREQUENCY, geneAnnots, geneToScoreMap, messenger, numGenesUsed, settings

Constructor Summary

Constructors

Constructor and Description
OraPvalGenerator(SettingsHolder settings, GeneScores geneScores, GeneAnnotations a, StatusViewer messenger)

Method Summary

Methods

Modifier and Type	Method and Description
protected GeneSetResult	classPval(Collection<Gene> genesAboveThresh, GeneSetTerm className) Get results for one class, based on class id.
void	computeCounts() Calculate numOverThreshold and numUnderThreshold for hypergeometric distribution.
Map<GeneSetTerm,GeneSetResult>	generateGeneSetResults() Compute the results for all the gene sets under consideration.
Collection<Gene>	getGenesAboveThreshold()
double	getGeneScoreThreshold()
int	getNumGenesOverThreshold() Always for the genes.
int	getNumGenesUnderThreshold() Always for genes.

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

Field Detail

geneScoreThreshold

protected double geneScoreThreshold

Constructor Detail

OraPvalGenerator

public OraPvalGenerator(SettingsHolder settings,
                GeneScores geneScores,
                GeneAnnotations a,
                StatusViewer messenger)

Parameters:

settings -

a -

messenger -

csc -

not -

nut -

inputSize -

Method Detail

computeCounts

public void computeCounts()

Calculate numOverThreshold and numUnderThreshold for hypergeometric distribution.

Parameters:

geneScores - The pvalues for the probes (no weights) or groups (weights)

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.

getGenesAboveThreshold

public Collection<Gene> getGenesAboveThreshold()

getGeneScoreThreshold

public double getGeneScoreThreshold()

getNumGenesOverThreshold

public int getNumGenesOverThreshold()

Always for the genes.

Returns:

getNumGenesUnderThreshold

public int getNumGenesUnderThreshold()

Always for genes.

Returns:

classPval

protected GeneSetResult classPval(Collection<Gene> genesAboveThresh,
                      GeneSetTerm className)

Get results for one class, based on class id. The other arguments are things that are not constant under permutations of the data.