ubic.erminej.analysis

Class GeneSetResamplingPvalGenerator

java.lang.Object

ubic.erminej.analysis.AbstractLongTask

ubic.erminej.analysis.AbstractGeneSetPvalGenerator

ubic.erminej.analysis.GeneSetResamplingPvalGenerator

Direct Known Subclasses:

ExperimentScoreQuickPvalGenerator

public class GeneSetResamplingPvalGenerator
extends AbstractGeneSetPvalGenerator

Generates gene set p values using the resampling-based 'experiment score' method of Pavlidis et al. 2002, or by using precision-recall curves (which are also calibrated by using resampling).

Version:

$Id: GeneSetResamplingPvalGenerator.java,v 1.17 2013/04/29 16:55:38 paul Exp $

Author:

Paul Pavlidis

Field Summary

Fields

Modifier and Type	Field and Description
protected GeneSetResamplingBackgroundDistributionGenerator	generator
protected Histogram	hist

Fields inherited from class ubic.erminej.analysis.AbstractGeneSetPvalGenerator

ALERT_UPDATE_FREQUENCY, geneAnnots, geneToScoreMap, messenger, numGenesUsed, settings

Constructor Summary

Constructors

Constructor and Description
GeneSetResamplingPvalGenerator(GeneSetResamplingPvalGenerator toclone, Map<Gene,Double> geneToScoreMap) Clone a generator; don't recompute the background.
GeneSetResamplingPvalGenerator(SettingsHolder settings, GeneAnnotations a, Map<Gene,Double> geneToScoreMap, StatusViewer messenger)

Method Summary

Methods

Modifier and Type	Method and Description
GeneSetResult	classPval(GeneSetTerm geneSetName) Get results for one class, based on class id.
Map<GeneSetTerm,Double>	classPvalGeneratorRaw() Same thing as classPval, but returns a more raw map of genesets to scores (pvalues) (see below) instead of adding them to the results object.
Map<GeneSetTerm,GeneSetResult>	generateGeneSetResults() Compute the results for all the gene sets under consideration.
protected Map<GeneSetTerm,GeneSetResult>	generateGeneSetResults(boolean useMultifunctionalityCorrection)
protected double	scoreToPval(int geneSetSize, double rawscore) Convert a raw score into a pvalue, based on background distribution

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

hist

protected Histogram hist

generator

protected GeneSetResamplingBackgroundDistributionGenerator generator

Constructor Detail

GeneSetResamplingPvalGenerator

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

Parameters:

settings -

a -

geneToScoreMap - already log-transformed, if requested.

messenger -

GeneSetResamplingPvalGenerator

public GeneSetResamplingPvalGenerator(GeneSetResamplingPvalGenerator toclone,
                              Map<Gene,Double> geneToScoreMap)

Clone a generator; don't recompute the background.

Parameters:

toclone -

geneToScoreMap -

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:

classPval

public GeneSetResult classPval(GeneSetTerm geneSetName)

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

Parameters:

geneSetName -

groupToPvalMap -

probesToPvals -

Returns:

classPvalGeneratorRaw

public Map<GeneSetTerm,Double> classPvalGeneratorRaw()

Same thing as classPval, but returns a more raw map of genesets to scores (pvalues) (see below) instead of adding them to the results object. This is used to get class pvalues for permutation analysis (W-Y correction)

scoreToPval

protected double scoreToPval(int geneSetSize,
                 double rawscore)

Convert a raw score into a pvalue, based on background distribution

Parameters:

geneSetSize - the size of the gene set that this score is for (used to identify which distribution to use)

rawscore - the raw score of the gene set

Returns:

double the pvalue for the raw score.