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)	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)

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)

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 copyMe,
                                                        boolean persist)

Redo

Parameters:

ee - the experiment

persist - whether to persist when done

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

Returns:

DEAs

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