ubic.erminej.analysis

Class GeneSetPvalRun

java.lang.Object

ubic.erminej.analysis.GeneSetPvalRun

public class GeneSetPvalRun
extends Object

Class that does all the work in doing gene set scoring. Holds the results as well.

Version:

$Id: GeneSetPvalRun.java,v 1.24 2013/05/05 20:08:48 paul Exp $

Author:

Paul Pavlidis

Constructor Summary

Constructors

Constructor and Description
GeneSetPvalRun(SettingsHolder settings, GeneAnnotations originalAnnots, StatusViewer messenger) Do a new analysis.
GeneSetPvalRun(SettingsHolder settings, GeneAnnotations originalAnnots, StatusViewer messenger, Map<GeneSetTerm,GeneSetResult> results, String name) Use this when we are loading in existing results from a file.
GeneSetPvalRun(SettingsHolder settings, GeneScores geneScores) Do a new analysis, starting from the bare essentials (correlation method not available) (simple API)

Method Summary

Methods

Modifier and Type	Method and Description
GeneAnnotations	getGeneData()
String	getGeneScoreColumnName()
Histogram	getHist()
double	getMultifunctionalityCorrelation()
double	getMultifunctionalityEnrichment() For ORA only.
double	getMultifunctionalityEnrichmentPvalue()
String	getName()
int	getNumAboveThreshold() ORA-only.
Map<GeneSetTerm,GeneSetResult>	getResults()
SettingsHolder	getSettings()
static List<GeneSetTerm>	getSortedClasses(Map<GeneSetTerm,GeneSetResult> results)
static List<GeneSetTerm>	getSortedClasses(Map<GeneSetTerm,GeneSetResult> results, boolean useMfCorrection)
boolean	hasBeenSavedToFile()
static List<GeneSetTerm>	populateRanks(Map<GeneSetTerm,GeneSetResult> results) Fill in the ranks
void	setName(String name)
void	setSavedToFile(boolean hasBeenSavedToFile)
String	toString()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

GeneSetPvalRun

public GeneSetPvalRun(SettingsHolder settings,
              GeneAnnotations originalAnnots,
              StatusViewer messenger)

Do a new analysis.

Parameters:

settings -

originalAnnots - - original!!! Will be pruned as necessary.

rawData -

geneScores -

messenger -

name - Name of the run

GeneSetPvalRun

public GeneSetPvalRun(SettingsHolder settings,
              GeneAnnotations originalAnnots,
              StatusViewer messenger,
              Map<GeneSetTerm,GeneSetResult> results,
              String name)
               throws IOException

Use this when we are loading in existing results from a file.

Parameters:

settings -

originalAnnots - - this does not need to be pruned by the Reader.

messenger -

results -

name - Name of the run

Throws:

IOException

GeneSetPvalRun

public GeneSetPvalRun(SettingsHolder settings,
              GeneScores geneScores)

Do a new analysis, starting from the bare essentials (correlation method not available) (simple API)

Method Detail

getSortedClasses

public static List<GeneSetTerm> getSortedClasses(Map<GeneSetTerm,GeneSetResult> results)

getSortedClasses

public static List<GeneSetTerm> getSortedClasses(Map<GeneSetTerm,GeneSetResult> results,
                                 boolean useMfCorrection)

Parameters:

-

useMfCorrection - Use the multifunctionality results stored.

Returns:

Ranked list. Removes any sets which are not scored.

populateRanks

public static List<GeneSetTerm> populateRanks(Map<GeneSetTerm,GeneSetResult> results)

Fill in the ranks

Returns:

sorted classes

getGeneData

public GeneAnnotations getGeneData()

getGeneScoreColumnName

public String getGeneScoreColumnName()

getHist

public Histogram getHist()

getMultifunctionalityCorrelation

public double getMultifunctionalityCorrelation()

getMultifunctionalityEnrichment

public double getMultifunctionalityEnrichment()

For ORA only.

Returns:

getMultifunctionalityEnrichmentPvalue

public double getMultifunctionalityEnrichmentPvalue()

getName

public String getName()

getNumAboveThreshold

public int getNumAboveThreshold()

ORA-only.

Returns:

getResults

public Map<GeneSetTerm,GeneSetResult> getResults()

Returns:

Map the results

getSettings

public SettingsHolder getSettings()

Returns:

the settings that were used during the analysis, which may be different than the current application-wide settings.

hasBeenSavedToFile

public boolean hasBeenSavedToFile()

setName

public void setName(String name)

setSavedToFile

public void setSavedToFile(boolean hasBeenSavedToFile)

toString

public String toString()

Overrides:

toString in class Object