Package ubic.gemma.core.analysis.expression.diff

Class DifferentialExpressionAnalyzerServiceImpl

java.lang.Object

ubic.gemma.core.analysis.expression.diff.DifferentialExpressionAnalyzerServiceImpl

All Implemented Interfaces:

DifferentialExpressionAnalyzerService

@Component
public class DifferentialExpressionAnalyzerServiceImpl
extends Object
implements DifferentialExpressionAnalyzerService

Differential expression service to run the differential expression analysis (and persist the results using the appropriate data access objects). Note that there is also a DifferentialExpressionAnalysisService (which handled CRUD for analyses). In contrast this _does_ the analysis.

Author:

keshav

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	DifferentialExpressionAnalyzerServiceImpl.AnalysisType	Defines the different types of analyses our linear modeling framework supports: GENERICLM - generic linear regression (interactions are omitted, but this could change) OSTTEST - one sample t-test OWA - one-way ANOVA TTEST - two sample t-test TWO_WAY_ANOVA_WITH_INTERACTION TWO_WAY_ANOVA_NO_INTERACTION

Constructor Summary

Constructors

Constructor	Description
DifferentialExpressionAnalyzerServiceImpl()

Method Summary

Modifier and Type	Method	Description
int	deleteAnalyses(ExpressionExperiment expressionExperiment)	Delete any differential expression analyses associated with the experiment.
void	deleteAnalysis(ExpressionExperiment expressionExperiment, DifferentialExpressionAnalysis existingAnalysis)	Deletes the given analysis.
void	deleteStatistics(ExpressionExperiment ee, DifferentialExpressionAnalysis analysis)	Remove old files which will otherwise be cruft.
Collection<ExpressionAnalysisResultSet>	extendAnalysis(ExpressionExperiment ee, DifferentialExpressionAnalysis toUpdate)	Like redo, but we don't save the results, we just add the full set of results to the analysis given.
Collection<DifferentialExpressionAnalysis>	getAnalyses(ExpressionExperiment expressionExperiment)
DifferentialExpressionAnalysis	persistAnalysis(ExpressionExperiment expressionExperiment, DifferentialExpressionAnalysis analysis, DifferentialExpressionAnalysisConfig config)	Made public for testing purposes only.
Collection<DifferentialExpressionAnalysis>	redoAnalysis(ExpressionExperiment ee, DifferentialExpressionAnalysis copyMe, boolean persist)	Redo
Collection<DifferentialExpressionAnalysis>	runDifferentialExpressionAnalyses(ExpressionExperiment expressionExperiment, DifferentialExpressionAnalysisConfig config)

Methods inherited from class java.lang.Object

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

Constructor Detail

DifferentialExpressionAnalyzerServiceImpl

public DifferentialExpressionAnalyzerServiceImpl()

Method Detail

deleteAnalyses

public int deleteAnalyses(ExpressionExperiment expressionExperiment)

Description copied from interface: DifferentialExpressionAnalyzerService

Delete any differential expression analyses associated with the experiment. Also deletes files associated with the analysis (e.g., results dumps) and associated hitlist sizes and pvalue distributions.

Specified by:

deleteAnalyses in interface DifferentialExpressionAnalyzerService

Parameters:

expressionExperiment - the experiment

Returns:

the number of analyses that were deleted

deleteAnalysis

public void deleteAnalysis(ExpressionExperiment expressionExperiment,
                           DifferentialExpressionAnalysis existingAnalysis)

Description copied from interface: DifferentialExpressionAnalyzerService

Deletes the given analysis. Also deletes files associated with the analysis. (e.g., results dumps)

Specified by:

deleteAnalysis in interface DifferentialExpressionAnalyzerService

Parameters:

expressionExperiment - the experiment

existingAnalysis - analysis

extendAnalysis

public Collection<ExpressionAnalysisResultSet> extendAnalysis(ExpressionExperiment ee,
                                                              DifferentialExpressionAnalysis toUpdate)

Description copied from interface: DifferentialExpressionAnalyzerService

Like redo, but we don't save the results, we just add the full set of results to the analysis given. If we want to keep these results, must call update on the old one.

Specified by:

extendAnalysis in interface DifferentialExpressionAnalyzerService

Parameters:

ee - the experiment

toUpdate - analysis

Returns:

collection of results

getAnalyses

public Collection<DifferentialExpressionAnalysis> getAnalyses(ExpressionExperiment expressionExperiment)

Specified by:

getAnalyses in interface DifferentialExpressionAnalyzerService

Parameters:

expressionExperiment - the experiment

Returns:

all DifferentialExpressionAnalysis entities for the experiment.

redoAnalysis

public Collection<DifferentialExpressionAnalysis> redoAnalysis(ExpressionExperiment ee,
                                                               DifferentialExpressionAnalysis copyMe,
                                                               boolean persist)

Description copied from interface: DifferentialExpressionAnalyzerService

Redo

Specified by:

redoAnalysis in interface DifferentialExpressionAnalyzerService

Parameters:

ee - the experiment

copyMe - analysis to base new one on whether the results should be persisted

persist - whether to persist when done

Returns:

DEAs

runDifferentialExpressionAnalyses

public Collection<DifferentialExpressionAnalysis> runDifferentialExpressionAnalyses(ExpressionExperiment expressionExperiment,
                                                                                    DifferentialExpressionAnalysisConfig config)

Specified by:

runDifferentialExpressionAnalyses in interface DifferentialExpressionAnalyzerService

Parameters:

expressionExperiment - the experiment

config - config

Returns:

persistent analyses.

persistAnalysis

public DifferentialExpressionAnalysis persistAnalysis(ExpressionExperiment expressionExperiment,
                                                      DifferentialExpressionAnalysis analysis,
                                                      DifferentialExpressionAnalysisConfig config)

Made public for testing purposes only.

Specified by:

persistAnalysis in interface DifferentialExpressionAnalyzerService

Parameters:

config - config

analysis - analysis

expressionExperiment - the experiment

Returns:

DEA

deleteStatistics

public void deleteStatistics(ExpressionExperiment ee,
                             DifferentialExpressionAnalysis analysis)

Remove old files which will otherwise be cruft.

Parameters:

ee - the experiment

analysis - analysis