ubic.erminej.analysis

Class CorrelationPvalGenerator

java.lang.Object

ubic.erminej.analysis.AbstractLongTask

ubic.erminej.analysis.AbstractGeneSetPvalGenerator

ubic.erminej.analysis.CorrelationPvalGenerator

public class CorrelationPvalGenerator
extends AbstractGeneSetPvalGenerator

Version:

$Id: CorrelationPvalGenerator.java,v 1.17 2012/05/27 02:54:30 paul Exp $

Author:

Shahmil Merchant, 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
CorrelationPvalGenerator(SettingsHolder settings, GeneAnnotations geneAnnots, DoubleMatrix<Probe,String> rawData, Histogram hist, StatusViewer messenger)

Method Summary

Methods

Modifier and Type	Method and Description
GeneSetResult	classPval(GeneSetTerm geneSetName)
boolean	containsRow(Probe name)
Map<GeneSetTerm,GeneSetResult>	generateGeneSetResults() Compute the results for all the gene sets under consideration.
double	geneSetMeanCorrel(DenseDoubleMatrix<String,String> correls) Note that we don't worry about replicates here - it would slow things down too much.
double	get_range()
int	getCacheHits()
DoubleMatrix<Probe,String>	getData()
int	getTests()
void	set_range(double range)
void	setCacheHits(int usedCache)
void	setGeneRepTreatment(SettingsHolder.MultiProbeHandling geneRepTreatment)
void	setHistogram(Histogram hist)
void	setTests(int tests)

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

CorrelationPvalGenerator

public CorrelationPvalGenerator(SettingsHolder settings,
                        GeneAnnotations geneAnnots,
                        DoubleMatrix<Probe,String> rawData,
                        Histogram hist,
                        StatusViewer messenger)

Parameters:

settings -

geneAnnots -

csc -

gon -

rawData -

hist -

Method Detail

classPval

public GeneSetResult classPval(GeneSetTerm geneSetName)

Parameters:

geneSetName -

Returns:

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

Parameters:

messenger -

Returns:

A map of GeneSetTerm to GeneSetResult.

containsRow

public boolean containsRow(Probe name)

Parameters:

name -

Returns:

geneSetMeanCorrel

public double geneSetMeanCorrel(DenseDoubleMatrix<String,String> correls)

Note that we don't worry about replicates here - it would slow things down too much.

Parameters:

correls -

Returns:

get_range

public double get_range()

getCacheHits

public int getCacheHits()

Returns:

Returns the usedCache.

getData

public DoubleMatrix<Probe,String> getData()

Returns:

getTests

public int getTests()

Returns:

Returns the tests.

set_range

public void set_range(double range)

setCacheHits

public void setCacheHits(int usedCache)

Parameters:

usedCache - The usedCache to set.

setGeneRepTreatment

public void setGeneRepTreatment(SettingsHolder.MultiProbeHandling geneRepTreatment)

Parameters:

geneRepTreatment -

setHistogram

public void setHistogram(Histogram hist)

Parameters:

hist -

setTests

public void setTests(int tests)

Parameters:

tests - The tests to set.