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

Interface DifferentialExpressionAnalysisDao

All Superinterfaces:

AnalysisDao<DifferentialExpressionAnalysis>, BaseDao<DifferentialExpressionAnalysis>, SingleExperimentAnalysisDao<DifferentialExpressionAnalysis>

public interface DifferentialExpressionAnalysisDao
extends SingleExperimentAnalysisDao<DifferentialExpressionAnalysis>

See Also:

DifferentialExpressionAnalysis

Method Summary

Modifier and Type	Method	Description
DifferentialExpressionAnalysis	findByExperimentAnalyzedAndId(BioAssaySet experimentAnalyzed, Long analysisId, boolean includeSubSets)	Find an analysis for the given experiment and identifier.
Map<Long,Collection<DifferentialExpressionAnalysis>>	findByExperimentAnalyzedId(Collection<Long> experimentAnalyzedId)
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)
Map<Long,List<DifferentialExpressionAnalysisValueObject>>	getAnalysesByExperimentIds(Collection<Long> expressionExperimentIds, int offset, int limit, boolean includeSubSets)
Collection<Long>	getExperimentsWithAnalysis(Collection<Long> experimentAnalyzedIds, boolean includeSubSets)
Collection<Long>	getExperimentsWithAnalysis(Taxon taxon)

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

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

Methods inherited from interface ubic.gemma.persistence.service.analysis.SingleExperimentAnalysisDao

existsByExperiment, findByExperiment, findByExperiments

Method Detail

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)

findByExperimentAnalyzedAndId

@Nullable
DifferentialExpressionAnalysis findByExperimentAnalyzedAndId(BioAssaySet experimentAnalyzed,
                                                             Long analysisId,
                                                             boolean includeSubSets)

Find an analysis for the given experiment and identifier.

findByExperimentAnalyzedId

Map<Long,Collection<DifferentialExpressionAnalysis>> findByExperimentAnalyzedId(Collection<Long> experimentAnalyzedId)

findExperimentsWithAnalyses

Collection<BioAssaySet> findExperimentsWithAnalyses(Gene gene)

getExperimentsWithAnalysis

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

getExperimentsWithAnalysis

Collection<Long> getExperimentsWithAnalysis(Taxon taxon)

getAnalysesByExperimentIds

Map<Long,List<DifferentialExpressionAnalysisValueObject>> getAnalysesByExperimentIds(Collection<Long> expressionExperimentIds,
                                                                                           int offset,
                                                                                           int limit,
                                                                                           boolean includeSubSets)