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

Interface DifferentialExpressionResultService

All Superinterfaces:

BaseReadOnlyService<DifferentialExpressionAnalysisResult>

All Known Implementing Classes:

DifferentialExpressionResultServiceImpl

public interface DifferentialExpressionResultService
extends BaseReadOnlyService<DifferentialExpressionAnalysisResult>

Main entry point to retrieve differential expression data.

Author:

kelsey

Method Summary

Modifier and Type	Method	Description
Map<BioAssaySetValueObject,List<DifferentialExpressionValueObject>>	findByExperimentAnalyzed(Collection<? extends BioAssaySet> experimentsAnalyzed, boolean includeSubSets, double threshold, int limit)
Map<BioAssaySetValueObject,List<DifferentialExpressionValueObject>>	findByGene(Gene gene, boolean useGene2Cs, boolean keepNonSpecificProbes)
Map<BioAssaySetValueObject,List<DifferentialExpressionValueObject>>	findByGene(Gene gene, boolean useGene2Cs, boolean keepNonSpecificProbes, double threshold, int limit)
Map<BioAssaySetValueObject,List<DifferentialExpressionValueObject>>	findByGeneAndExperimentAnalyzed(Gene gene, boolean useGene2Cs, boolean keepNonSpecificProbes, Collection<? extends BioAssaySet> experimentsAnalyzed, boolean includeSubSets)
Map<BioAssaySetValueObject,List<DifferentialExpressionValueObject>>	findByGeneAndExperimentAnalyzed(Gene gene, boolean useGene2Cs, boolean keepNonSpecificProbes, Collection<? extends BioAssaySet> experimentsAnalyzed, boolean includeSubSets, double threshold, int limit)
List<DifferentialExpressionAnalysisResult>	findByGeneAndExperimentAnalyzedIds(Gene gene, boolean useGene2Cs, boolean keepNonSpecific, Collection<Long> experimentAnalyzedIds, boolean includeSubSets, Map<DifferentialExpressionAnalysisResult,Long> sourceExperimentIdMap, Map<DifferentialExpressionAnalysisResult,Long> experimentAnalyzedIdMap, Map<DifferentialExpressionAnalysisResult,Baseline> baselineMap, double threshold, boolean initializeFactorValues)
List<DifferentialExpressionValueObject>	findByResultSet(ExpressionAnalysisResultSet ar, double threshold, int maxResultsToReturn, int minNumberOfResults)
Map<Long,ContrastsValueObject>	findContrastsByAnalysisResultIds(Collection<Long> ids)
Map<Long,Map<Long,DiffExprGeneSearchResult>>	findGeneResultsByResultSetIdsAndGeneIds(Collection<DiffExResultSetSummaryValueObject> resultSets, Collection<Long> geneIds)

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

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

Method Details

findByExperimentAnalyzed

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_VALUE_OBJECT_MAP_READ"})
Map<BioAssaySetValueObject,List<DifferentialExpressionValueObject>> findByExperimentAnalyzed(Collection<? extends BioAssaySet> experimentsAnalyzed,
 boolean includeSubSets,
 double threshold,
 int limit)

See Also:

• DifferentialExpressionResultDao.findByExperimentAnalyzed(Collection, boolean, double, int)

findByGene

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_VALUE_OBJECT_MAP_READ"})
Map<BioAssaySetValueObject,List<DifferentialExpressionValueObject>> findByGene(Gene gene,
 boolean useGene2Cs,
 boolean keepNonSpecificProbes)

See Also:

• DifferentialExpressionResultDao.findByGene(Gene, boolean, boolean)

findByGene

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_VALUE_OBJECT_MAP_READ"})
Map<BioAssaySetValueObject,List<DifferentialExpressionValueObject>> findByGene(Gene gene,
 boolean useGene2Cs,
 boolean keepNonSpecificProbes,
 double threshold,
 int limit)

See Also:

• DifferentialExpressionResultDao.findByGene(Gene, boolean, boolean, double, int)

findByGeneAndExperimentAnalyzedIds

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_DIFFERENTIAL_EXPRESSION_ANALYSIS_RESULT_COLLECTION_READ"})
List<DifferentialExpressionAnalysisResult> findByGeneAndExperimentAnalyzedIds(Gene gene,
 boolean useGene2Cs,
 boolean keepNonSpecific,
 Collection<Long> experimentAnalyzedIds,
 boolean includeSubSets,
 Map<DifferentialExpressionAnalysisResult,Long> sourceExperimentIdMap,
 Map<DifferentialExpressionAnalysisResult,Long> experimentAnalyzedIdMap,
 Map<DifferentialExpressionAnalysisResult,Baseline> baselineMap,
 double threshold,
 boolean initializeFactorValues)

See Also:

• DifferentialExpressionResultDao.findByGeneAndExperimentAnalyzed(Gene, Collection, boolean, Map, Map, Map, double, boolean, boolean, boolean)

findByGeneAndExperimentAnalyzed

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_VALUE_OBJECT_MAP_READ"})
Map<BioAssaySetValueObject,List<DifferentialExpressionValueObject>> findByGeneAndExperimentAnalyzed(Gene gene,
 boolean useGene2Cs,
 boolean keepNonSpecificProbes,
 Collection<? extends BioAssaySet> experimentsAnalyzed,
 boolean includeSubSets)

See Also:

• DifferentialExpressionResultDao.findByGeneAndExperimentAnalyzed(Gene, boolean, boolean, Collection, boolean)

findByGeneAndExperimentAnalyzed

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_VALUE_OBJECT_MAP_READ"})
Map<BioAssaySetValueObject,List<DifferentialExpressionValueObject>> findByGeneAndExperimentAnalyzed(Gene gene,
 boolean useGene2Cs,
 boolean keepNonSpecificProbes,
 Collection<? extends BioAssaySet> experimentsAnalyzed,
 boolean includeSubSets,
 double threshold,
 int limit)

See Also:

• DifferentialExpressionResultDao.findByGeneAndExperimentAnalyzed(Gene, boolean, boolean, Collection, boolean, double, int)

findGeneResultsByResultSetIdsAndGeneIds

Map<Long,Map<Long,DiffExprGeneSearchResult>> findGeneResultsByResultSetIdsAndGeneIds(Collection<DiffExResultSetSummaryValueObject> resultSets,
 Collection<Long> geneIds)

See Also:

• DifferentialExpressionResultDao.findGeneResultsByResultSetIdsAndGeneIds(Collection, Collection)

findByResultSet

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
List<DifferentialExpressionValueObject> findByResultSet(ExpressionAnalysisResultSet ar,
 double threshold,
 int maxResultsToReturn,
 int minNumberOfResults)

See Also:

• DifferentialExpressionResultDao.findByResultSet(ExpressionAnalysisResultSet, double, int, int)

findContrastsByAnalysisResultIds

Map<Long,ContrastsValueObject> findContrastsByAnalysisResultIds(Collection<Long> ids)

See Also:

• DifferentialExpressionResultDao.findContrastsByAnalysisResultIds(Collection)