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
Integer	countDownregulated(ExpressionAnalysisResultSet par, double threshold)
Integer	countProbesMeetingThreshold(ExpressionAnalysisResultSet ears, double threshold)
Integer	countUpregulated(ExpressionAnalysisResultSet par, double threshold)
Collection<DifferentialExpressionAnalysis>	find(Gene gene, ExpressionAnalysisResultSet resultSet, double threshold)
Map<Long,Collection<DifferentialExpressionAnalysis>>	findByExperimentIds(Collection<Long> investigationIds)
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<BioAssaySet>	findExperimentsWithAnalyses(Gene gene)
Map<ExpressionExperiment,Collection<DifferentialExpressionAnalysis>>	getAnalyses(Collection<? extends BioAssaySet> expressionExperiments)
Map<Long,List<DifferentialExpressionAnalysisValueObject>>	getAnalysesByExperimentIds(Collection<Long> expressionExperimentIds, int offset, int limit)
Collection<Long>	getExperimentsWithAnalysis(Collection<Long> idsToFilter)
Collection<Long>	getExperimentsWithAnalysis(Taxon taxon)

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

existsByExperiment, findByName, findByTaxon

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

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

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

findByExperiment, findByExperiments

Method Detail

countDownregulated

Integer countDownregulated(ExpressionAnalysisResultSet par,
                           double threshold)

Parameters:

threshold - for corrected pvalue. Results may not be accurate for 'unreasonable' thresholds.

countProbesMeetingThreshold

Integer countProbesMeetingThreshold(ExpressionAnalysisResultSet ears,
                                    double threshold)

Parameters:

threshold - for corrected pvalue. Results may not be accurate for 'unreasonable' thresholds.

countUpregulated

Integer countUpregulated(ExpressionAnalysisResultSet par,
                         double threshold)

Parameters:

threshold - for corrected pvalue. Results may not be accurate for 'unreasonable' thresholds.

find

Collection<DifferentialExpressionAnalysis> find(Gene gene,
                                                ExpressionAnalysisResultSet resultSet,
                                                double threshold)

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)

findByExperimentIds

Map<Long,Collection<DifferentialExpressionAnalysis>> findByExperimentIds(Collection<Long> investigationIds)

findExperimentsWithAnalyses

Collection<BioAssaySet> findExperimentsWithAnalyses(Gene gene)

getAnalyses

Map<ExpressionExperiment,Collection<DifferentialExpressionAnalysis>> getAnalyses(Collection<? extends BioAssaySet> expressionExperiments)

getExperimentsWithAnalysis

Collection<Long> getExperimentsWithAnalysis(Collection<Long> idsToFilter)

getExperimentsWithAnalysis

Collection<Long> getExperimentsWithAnalysis(Taxon taxon)

getAnalysesByExperimentIds

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