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

Interface DifferentialExpressionAnalyzerService

All Known Implementing Classes:

DifferentialExpressionAnalyzerServiceImpl

public interface DifferentialExpressionAnalyzerService

Author:

Paul

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.
Collection<ExpressionAnalysisResultSet>	extendAnalysis(ExpressionExperiment ee, DifferentialExpressionAnalysis toUpdate, DifferentialExpressionAnalysisConfig config)	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)

Method Detail

deleteAnalyses

int deleteAnalyses(ExpressionExperiment expressionExperiment)

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.

Parameters:

expressionExperiment - the experiment

Returns:

the number of analyses that were deleted

deleteAnalysis

void deleteAnalysis(ExpressionExperiment expressionExperiment,
                    DifferentialExpressionAnalysis existingAnalysis)

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

Parameters:

expressionExperiment - the experiment

existingAnalysis - analysis

extendAnalysis

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

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.

Parameters:

ee - the experiment

toUpdate - analysis

Returns:

collection of results

getAnalyses

Collection<DifferentialExpressionAnalysis> getAnalyses(ExpressionExperiment expressionExperiment)

Parameters:

expressionExperiment - the experiment

Returns:

all DifferentialExpressionAnalysis entities for the experiment.

redoAnalysis

Collection<DifferentialExpressionAnalysis> redoAnalysis(ExpressionExperiment ee,
                                                        DifferentialExpressionAnalysis dea)

Redo an analysis.

See Also:

redoAnalysis(ExpressionExperiment, DifferentialExpressionAnalysis, DifferentialExpressionAnalysisConfig)

redoAnalysis

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

Redo an analysis.

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

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

Redo multiple analyses.

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:

redoAnalysis(ExpressionExperiment, DifferentialExpressionAnalysis, DifferentialExpressionAnalysisConfig)

runDifferentialExpressionAnalyses

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

Parameters:

expressionExperiment - the experiment

config - config

Returns:

persistent analyses.

persistAnalysis

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

Made public for testing purposes only.

Parameters:

expressionExperiment - the experiment

config - config

analysis - analysis

Returns:

persistent analysis