Interface DifferentialExpressionAnalyzerService
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- All Known Implementing Classes:
DifferentialExpressionAnalyzerServiceImpl
public interface DifferentialExpressionAnalyzerService
- Author:
- Paul
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Method Summary
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Method Detail
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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
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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 experimentexistingAnalysis
- analysis
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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 experimenttoUpdate
- analysis- Returns:
- collection of results
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getAnalyses
Collection<DifferentialExpressionAnalysis> getAnalyses(ExpressionExperiment expressionExperiment)
- Parameters:
expressionExperiment
- the experiment- Returns:
- all DifferentialExpressionAnalysis entities for the experiment.
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redoAnalysis
Collection<DifferentialExpressionAnalysis> redoAnalysis(ExpressionExperiment ee, DifferentialExpressionAnalysis copyMe, boolean persist)
Redo- Parameters:
ee
- the experimentpersist
- whether to persist when donecopyMe
- analysis to base new one on whether the results should be persisted- Returns:
- DEAs
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runDifferentialExpressionAnalyses
Collection<DifferentialExpressionAnalysis> runDifferentialExpressionAnalyses(ExpressionExperiment expressionExperiment, DifferentialExpressionAnalysisConfig config)
- Parameters:
expressionExperiment
- the experimentconfig
- config- Returns:
- persistent analyses.
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persistAnalysis
DifferentialExpressionAnalysis persistAnalysis(ExpressionExperiment expressionExperiment, DifferentialExpressionAnalysis analysis, DifferentialExpressionAnalysisConfig config)
Made public for testing purposes only.- Parameters:
expressionExperiment
- the experimentconfig
- configanalysis
- analysis- Returns:
- persistent analysis
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