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)	Given a list of experiments and a threshold value finds all the probes that met the cut off in the given experiments
Map<BioAssaySetValueObject,List<DifferentialExpressionValueObject>>	findByGene(Gene gene, boolean keepNonSpecificProbes)	Returns a map of a collection of DifferentialExpressionAnalysisResults keyed by ExpressionExperiment.
Map<BioAssaySetValueObject,List<DifferentialExpressionValueObject>>	findByGene(Gene gene, boolean keepNonSpecificProbes, double threshold, int limit)	Find differential expression for a gene, exceeding a given significance level (using the corrected pvalue field)
Map<BioAssaySetValueObject,List<DifferentialExpressionValueObject>>	findByGeneAndExperimentAnalyzed(Gene gene, boolean keepNonSpecificProbes, Collection<? extends BioAssaySet> experimentsAnalyzed, boolean includeSubSets)	Returns a map of a collection of DifferentialExpressionAnalysisResults keyed by ExpressionExperiment.
Map<BioAssaySetValueObject,List<DifferentialExpressionValueObject>>	findByGeneAndExperimentAnalyzed(Gene gene, boolean keepNonSpecificProbes, Collection<? extends BioAssaySet> experimentsAnalyzed, boolean includeSubSets, double threshold, int limit)	Find differential expression for a gene in given data sets, exceeding a given significance level (using the corrected pvalue field)
List<DifferentialExpressionAnalysisResult>	findByGeneAndExperimentAnalyzedIds(Gene gene, boolean keepNonSpecific, Collection<Long> experimentAnalyzedIds, boolean includeSubSets, Map<DifferentialExpressionAnalysisResult,Long> sourceExperimentIdMap, Map<DifferentialExpressionAnalysisResult,Long> experimentAnalyzedIdMap, Map<DifferentialExpressionAnalysisResult,Baseline> baselineMap, double threshold, boolean initializeFactorValues)
Map<Long,Map<Long,DiffExprGeneSearchResult>>	findDiffExAnalysisResultIdsInResultSets(Collection<DiffExResultSetSummaryValueObject> resultSets, Collection<Long> geneIds)	Retrieve differential expression results in bulk.
List<DifferentialExpressionValueObject>	findInResultSet(ExpressionAnalysisResultSet ar, Double threshold, int maxResultsToReturn, int minNumberOfResults)
Map<Long,ContrastsValueObject>	loadContrastDetailsForResults(Collection<Long> ids)

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

countAll, find, findOrFail, getElementClass, load, load, loadAll, 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)

Given a list of experiments and a threshold value finds all the probes that met the cut off in the given experiments

Parameters:

experimentsAnalyzed - ees

includeSubSets - if true, include the subsets of the experiments analyzed

threshold - threshold

limit - limit

Returns:

map to diff ex VOs

findByGene

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

Returns a map of a collection of DifferentialExpressionAnalysisResults keyed by ExpressionExperiment.

Parameters:

gene - gene

keepNonSpecificProbes -

Returns:

map to diff ex VOs

findByGene

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

Find differential expression for a gene, exceeding a given significance level (using the corrected pvalue field)

Parameters:

gene - gene

keepNonSpecificProbes -

threshold - threshold

limit - limit

Returns:

map to diff ex VOs

findByGeneAndExperimentAnalyzedIds

@Secured("IS_AUTHENTICATED_ANONYMOUSLY")
List<DifferentialExpressionAnalysisResult> findByGeneAndExperimentAnalyzedIds(Gene gene,
 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)

findByGeneAndExperimentAnalyzed

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

Returns a map of a collection of DifferentialExpressionAnalysisResults keyed by ExpressionExperiment.

Parameters:

gene - gene

keepNonSpecificProbes -

experimentsAnalyzed - ees

includeSubSets -

Returns:

map to diff ex VOs

findByGeneAndExperimentAnalyzed

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

Find differential expression for a gene in given data sets, exceeding a given significance level (using the corrected pvalue field)

Parameters:

gene - gene

keepNonSpecificProbes -

experimentsAnalyzed - ees

includeSubSets -

threshold - threshold

limit - limit

Returns:

map to diff ex VOs

findDiffExAnalysisResultIdsInResultSets

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

Retrieve differential expression results in bulk. This is an important method for the differential expression interfaces.

Parameters:

resultSets - result sets

geneIds - gene ids

Returns:

map of resultset IDs to map of gene id to differential expression results.

findInResultSet

List<DifferentialExpressionValueObject> findInResultSet(ExpressionAnalysisResultSet ar,
 Double threshold,
 int maxResultsToReturn,
 int minNumberOfResults)

loadContrastDetailsForResults

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

Parameters:

ids - ids

Returns:

map of result to contrasts value object.