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

Interface ExpressionAnalysisResultSetService

All Superinterfaces:

AnalysisResultSetService<DifferentialExpressionAnalysisResult,ExpressionAnalysisResultSet>, BaseReadOnlyService<ExpressionAnalysisResultSet>, BaseVoEnabledService<ExpressionAnalysisResultSet,DifferentialExpressionAnalysisResultSetValueObject>, FilteringService<ExpressionAnalysisResultSet>, FilteringVoEnabledService<ExpressionAnalysisResultSet,DifferentialExpressionAnalysisResultSetValueObject>

All Known Implementing Classes:

ExpressionAnalysisResultSetServiceImpl

public interface ExpressionAnalysisResultSetService
extends AnalysisResultSetService<DifferentialExpressionAnalysisResult,ExpressionAnalysisResultSet>, FilteringVoEnabledService<ExpressionAnalysisResultSet,DifferentialExpressionAnalysisResultSetValueObject>

Method Summary

Modifier and Type	Method	Description
long	countResults(ExpressionAnalysisResultSet ears)
long	countResults(ExpressionAnalysisResultSet ears, double threshold)
Slice<DifferentialExpressionAnalysisResultSetValueObject>	findByBioAssaySetInAndDatabaseEntryInLimit(Collection<BioAssaySet> bioAssaySets, Collection<DatabaseEntry> externalIds, Filters filters, int offset, int limit, Sort sort)
Baseline	getBaseline(ExpressionAnalysisResultSet ears)
Map<ExpressionAnalysisResultSet,Baseline>	getBaselinesForInteractions(Set<ExpressionAnalysisResultSet> resultSets, boolean initializeFactorValues)
Map<Long,Baseline>	getBaselinesForInteractionsByIds(Collection<Long> rsIds, boolean initializeFactorValues)
Histogram	loadPvalueDistribution(ExpressionAnalysisResultSet resulSet)
Map<Long,List<Gene>>	loadResultIdToGenesMap(ExpressionAnalysisResultSet ears)
DifferentialExpressionAnalysisResultSetValueObject	loadValueObjectWithResults(ExpressionAnalysisResultSet ears, boolean includeFactorValuesInContrasts, boolean queryByResult, boolean includeTaxonInGenes)
ExpressionAnalysisResultSet	loadWithAnalysis(Long id)
ExpressionAnalysisResultSet	loadWithExperimentAnalyzed(Long id)
ExpressionAnalysisResultSet	loadWithResultsAndContrasts(Long value)
ExpressionAnalysisResultSet	loadWithResultsAndContrasts(Long value, double threshold, int offset, int limit)
ExpressionAnalysisResultSet	loadWithResultsAndContrasts(Long value, int offset, int limit)
ExpressionAnalysisResultSet	thaw(ExpressionAnalysisResultSet e)

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

countAll, find, findOrFail, getElementClass, load, load, loadAll, loadOrFail, loadOrFail, loadOrFail, loadOrFail

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

loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

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

count, getFilter, getFilter, getFilter, getFilter, getFilter, getFilter, getFilterableProperties, getFilterablePropertyAllowedValues, getFilterablePropertyConfigAttributes, getFilterablePropertyDescription, getFilterablePropertyIsUsingSubquery, getFilterablePropertyResolvableAllowedValuesLabels, getFilterablePropertyType, getIdentifierPropertyName, getSort, load, load, loadIds

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

loadValueObjects, loadValueObjects

Method Detail

loadWithAnalysis

ExpressionAnalysisResultSet loadWithAnalysis(Long id)

loadWithResultsAndContrasts

ExpressionAnalysisResultSet loadWithResultsAndContrasts(Long value)

loadWithResultsAndContrasts

ExpressionAnalysisResultSet loadWithResultsAndContrasts(Long value,
                                                        int offset,
                                                        int limit)

loadWithResultsAndContrasts

ExpressionAnalysisResultSet loadWithResultsAndContrasts(Long value,
                                                        double threshold,
                                                        int offset,
                                                        int limit)

countResults

long countResults(ExpressionAnalysisResultSet ears)

countResults

long countResults(ExpressionAnalysisResultSet ears,
                  double threshold)

thaw

@CheckReturnValue
ExpressionAnalysisResultSet thaw(ExpressionAnalysisResultSet e)

loadWithExperimentAnalyzed

ExpressionAnalysisResultSet loadWithExperimentAnalyzed(Long id)

loadValueObjectWithResults

DifferentialExpressionAnalysisResultSetValueObject loadValueObjectWithResults(ExpressionAnalysisResultSet ears,
                                                                              boolean includeFactorValuesInContrasts,
                                                                              boolean queryByResult,
                                                                              boolean includeTaxonInGenes)

loadResultIdToGenesMap

Map<Long,List<Gene>> loadResultIdToGenesMap(ExpressionAnalysisResultSet ears)

findByBioAssaySetInAndDatabaseEntryInLimit

Slice<DifferentialExpressionAnalysisResultSetValueObject> findByBioAssaySetInAndDatabaseEntryInLimit(@Nullable
                                                                                                     Collection<BioAssaySet> bioAssaySets,
                                                                                                     @Nullable
                                                                                                     Collection<DatabaseEntry> externalIds,
                                                                                                     @Nullable
                                                                                                     Filters filters,
                                                                                                     int offset,
                                                                                                     int limit,
                                                                                                     @Nullable
                                                                                                     Sort sort)

getBaseline

Baseline getBaseline(ExpressionAnalysisResultSet ears)

getBaselinesForInteractions

Map<ExpressionAnalysisResultSet,Baseline> getBaselinesForInteractions(Set<ExpressionAnalysisResultSet> resultSets,
                                                                            boolean initializeFactorValues)

getBaselinesForInteractionsByIds

Map<Long,Baseline> getBaselinesForInteractionsByIds(Collection<Long> rsIds,
                                                          boolean initializeFactorValues)

loadPvalueDistribution

@Nullable
Histogram loadPvalueDistribution(ExpressionAnalysisResultSet resulSet)