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

Class DifferentialExpressionAnalyzerServiceImpl

java.lang.Object

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

All Implemented Interfaces:

DifferentialExpressionAnalyzerService

@Component
@Transactional(propagation=NEVER)
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

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.
int	deleteAnalyses(ExpressionExperiment ee, Collection<DifferentialExpressionAnalysis> analysesToDelete)	Delete the specified 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, DifferentialExpressionAnalysisConfig baseConfig)	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>	redoAnalyses(ExpressionExperiment ee, Collection<DifferentialExpressionAnalysis> deas, DifferentialExpressionAnalysisConfig config, boolean ignoreFailingAnalyses)	Redo multiple analyses.
Collection<DifferentialExpressionAnalysis>	redoAnalysis(ExpressionExperiment ee, DifferentialExpressionAnalysis dea)	Redo an analysis.
Collection<DifferentialExpressionAnalysis>	redoAnalysis(ExpressionExperiment ee, DifferentialExpressionAnalysis dea, DifferentialExpressionAnalysisConfig config)	Redo an analysis.
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 Details

DifferentialExpressionAnalyzerServiceImpl

public DifferentialExpressionAnalyzerServiceImpl()

Method Details

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

deleteAnalyses

public int deleteAnalyses(ExpressionExperiment ee,
 Collection<DifferentialExpressionAnalysis> analysesToDelete)

Description copied from interface: DifferentialExpressionAnalyzerService

Delete the specified differential expression analyses associated with the experiment.

Specified by:

deleteAnalyses in interface DifferentialExpressionAnalyzerService

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,
 DifferentialExpressionAnalysisConfig baseConfig)

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 dea)

Description copied from interface: DifferentialExpressionAnalyzerService

Redo an analysis.

Specified by:

redoAnalysis in interface DifferentialExpressionAnalyzerService

See Also:

• DifferentialExpressionAnalyzerService.redoAnalysis(ExpressionExperiment, DifferentialExpressionAnalysis, DifferentialExpressionAnalysisConfig)

redoAnalysis

public Collection<DifferentialExpressionAnalysis> redoAnalysis(ExpressionExperiment ee,
 DifferentialExpressionAnalysis dea,
 DifferentialExpressionAnalysisConfig config)

Description copied from interface: DifferentialExpressionAnalyzerService

Redo an analysis.

Specified by:

redoAnalysis in interface DifferentialExpressionAnalyzerService

Parameters:

ee - the experiment

dea - analysis to base new one on

config - configuration for the analysis, factors and interactions will be ignored, but all other settings apply as usual

Returns:

DEAs

redoAnalyses

public Collection<DifferentialExpressionAnalysis> redoAnalyses(ExpressionExperiment ee,
 Collection<DifferentialExpressionAnalysis> deas,
 DifferentialExpressionAnalysisConfig config,
 boolean ignoreFailingAnalyses)

Description copied from interface: DifferentialExpressionAnalyzerService

Redo multiple analyses.

Specified by:

redoAnalyses in interface DifferentialExpressionAnalyzerService

Parameters:

ignoreFailingAnalyses - if true, analyses that fail will not be reported as errors, but will be skipped. Note that if all analyses fail, a AllAnalysesFailedException will be raised.

See Also:

• DifferentialExpressionAnalyzerService.redoAnalysis(ExpressionExperiment, DifferentialExpressionAnalysis, DifferentialExpressionAnalysisConfig)

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:

expressionExperiment - the experiment

analysis - analysis

config - config

Returns:

DEA

deleteStatistics

public void deleteStatistics(ExpressionExperiment ee,
 DifferentialExpressionAnalysis analysis)

Remove old files which will otherwise be cruft.

Parameters:

ee - the experiment

analysis - analysis