Package ubic.gemma.persistence.service.analysis.expression.diff

Interface DifferentialExpressionAnalysisDao

All Superinterfaces:

AnalysisDao<DifferentialExpressionAnalysis>, BaseDao<DifferentialExpressionAnalysis>

public interface DifferentialExpressionAnalysisDao
extends AnalysisDao<DifferentialExpressionAnalysis>

See Also:

• DifferentialExpressionAnalysis

Method Summary

Modifier and Type	Method	Description
Collection<DifferentialExpressionAnalysis>	findByExperiment(ExpressionExperiment experiment, boolean includeSubSets)	Find by associated ExpressionExperiment.
Collection<DifferentialExpressionAnalysis>	findByExperimentAnalyzed(BioAssaySet experimentAnalyzed)	Find by associated experiment via SingleExperimentAnalysis.getExperimentAnalyzed().
DifferentialExpressionAnalysis	findByExperimentAndAnalysisId(ExpressionExperiment experimentAnalyzed, boolean includeSubSets, Long analysisId)	Find an analysis for the given experiment and identifier.
Map<ExpressionExperiment,Collection<DifferentialExpressionAnalysis>>	findByExperimentIds(Collection<Long> experimentIds, boolean includeSubSets, Map<Long,Collection<Long>> arrayDesignUsed, Map<Long,Collection<FactorValue>> ee2fv)	Retrieve analysis for the given experiment or experiment subset IDs.
Map<ExpressionExperiment,Collection<DifferentialExpressionAnalysis>>	findByExperiments(Collection<ExpressionExperiment> experiments, boolean includeSubSets)	Find by associated ExpressionExperiments.
Collection<DifferentialExpressionAnalysis>	findByFactor(ExperimentalFactor ef)	Retrieve analyses associated with the factor, either through the subset factor or as factors for result sets.
Collection<DifferentialExpressionAnalysis>	findByFactors(Collection<ExperimentalFactor> experimentalFactors)
Collection<DifferentialExpressionAnalysis>	findByName(String name)
Collection<BioAssaySet>	findExperimentsWithAnalyses(Gene gene)	Find experiments (or subsets) that have differential expression analyses for the given gene.
Collection<Long>	getExperimentsWithAnalysis(Collection<Long> eeIds, boolean includeSubSets)

Methods inherited from interface ubic.gemma.persistence.service.BaseDao

countAll, create, create, find, findOrCreate, getElementClass, load, load, loadAll, loadReference, loadReference, reload, reload, remove, remove, save, save, streamAll, streamAll, update, update

Method Details

findByExperiment

Collection<DifferentialExpressionAnalysis> findByExperiment(ExpressionExperiment experiment,
 boolean includeSubSets)

Find by associated ExpressionExperiment.

Parameters:

includeSubSets - include subsets of the specified experiment

findByExperimentAnalyzed

Collection<DifferentialExpressionAnalysis> findByExperimentAnalyzed(BioAssaySet experimentAnalyzed)

Find by associated experiment via SingleExperimentAnalysis.getExperimentAnalyzed().

findByExperiments

Map<ExpressionExperiment,Collection<DifferentialExpressionAnalysis>> findByExperiments(Collection<ExpressionExperiment> experiments,
 boolean includeSubSets)

Find by associated ExpressionExperiments.

Parameters:

includeSubSets - include subsets of the specified experiments

Returns:

map to analyses grouped by source experiment

findByExperimentIds

Map<ExpressionExperiment,Collection<DifferentialExpressionAnalysis>> findByExperimentIds(Collection<Long> experimentIds,
 boolean includeSubSets,
 @Nullable
 Map<Long,Collection<Long>> arrayDesignUsed,
 @Nullable
 Map<Long,Collection<FactorValue>> ee2fv)

Retrieve analysis for the given experiment or experiment subset IDs.

Results are grouped by source experiment.

Parameters:

experimentIds - experiment IDs (no subset allowed!)

includeSubSets - include analyses for subsets of the requested experiment IDs

arrayDesignUsed - a map of experiments or subset ID to array design IDs used

ee2fv - a map of experiments or subset ID to factor values used

Returns:

map to analyses grouped by source experiment

findByName

Collection<DifferentialExpressionAnalysis> findByName(String name)

findByFactor

Collection<DifferentialExpressionAnalysis> findByFactor(ExperimentalFactor ef)

Retrieve analyses associated with the factor, either through the subset factor or as factors for result sets.

findByFactors

Collection<DifferentialExpressionAnalysis> findByFactors(Collection<ExperimentalFactor> experimentalFactors)

See Also:

• findByFactor(ExperimentalFactor)

findByExperimentAndAnalysisId

@Nullable
DifferentialExpressionAnalysis findByExperimentAndAnalysisId(ExpressionExperiment experimentAnalyzed,
 boolean includeSubSets,
 Long analysisId)

Find an analysis for the given experiment and identifier.

findExperimentsWithAnalyses

Collection<BioAssaySet> findExperimentsWithAnalyses(Gene gene)

Find experiments (or subsets) that have differential expression analyses for the given gene.

getExperimentsWithAnalysis

Collection<Long> getExperimentsWithAnalysis(Collection<Long> eeIds,
 boolean includeSubSets)