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>	findByExperimentAnalyzed(BioAssaySet experimentAnalyzed)
Collection<DifferentialExpressionAnalysis>	findByExperimentAnalyzed(ExpressionExperiment experiment, boolean includeSubSets)	Find by associated experiment via SingleExperimentAnalysis.getExperimentAnalyzed().
Map<Long,Collection<DifferentialExpressionAnalysis>>	findByExperimentAnalyzedId(Collection<Long> experimentAnalyzedId)
DifferentialExpressionAnalysis	findByExperimentAndAnalysisId(ExpressionExperiment experimentAnalyzed, Long analysisId, boolean includeSubSets)	Find an analysis for the given experiment and identifier.
Map<BioAssaySet,Collection<DifferentialExpressionAnalysis>>	findByExperimentsAnalyzed(Collection<ExpressionExperiment> experiments, boolean includeSubSets)	Given a collection of experiments returns a Map of Analysis --> collection of Experiments The collection of investigations returned by the map will include all the investigations for the analysis key iff one of the investigations for that analysis was in the given collection started with
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> eeIds, 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

Method Details

findByExperimentAnalyzed

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

Find by associated experiment via SingleExperimentAnalysis.getExperimentAnalyzed().

Parameters:

includeSubSets - include subsets of the specified experiments

findByExperimentAnalyzed

Collection<DifferentialExpressionAnalysis> findByExperimentAnalyzed(BioAssaySet experimentAnalyzed)

findByExperimentsAnalyzed

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

Given a collection of experiments returns a Map of Analysis --> collection of Experiments The collection of investigations returned by the map will include all the investigations for the analysis key iff one of the investigations for that analysis was in the given collection started with

Parameters:

experiments - experiments

includeSubSets - include subsets of the specified experiments

Returns:

map to analyses

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,
 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> eeIds,
 boolean includeSubSets)

getExperimentsWithAnalysis

Collection<Long> getExperimentsWithAnalysis(Taxon taxon)

getAnalysesByExperimentIds

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