Interface DifferentialExpressionResultDao
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- All Superinterfaces:
BaseDao<DifferentialExpressionAnalysisResult>
- All Known Implementing Classes:
DifferentialExpressionResultDaoImpl
public interface DifferentialExpressionResultDao extends BaseDao<DifferentialExpressionAnalysisResult>
- See Also:
DifferentialExpressionAnalysisResult
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>>
find(Gene gene, double threshold, int limit)
Find differential expression for a gene, exceeding a given significance level (using the corrected pvalue field)Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>>
findByExperimentAnalyzed(Collection<Long> experimentsAnalyzed, 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 experimentsMap<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>>
findByGene(Gene gene)
Find differential expression results for a given gene, grouped by experiment.Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>>
findByGeneAndExperimentAnalyzed(Gene gene, Collection<Long> experimentsAnalyzed)
Find differential expression results for a given gene and set of experiments, grouped by experiment.Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>>
findByGeneAndExperimentAnalyzed(Gene gene, Collection<Long> experimentsAnalyzed, double threshold, int limit)
Find differential expression for a gene in given data sets, exceeding a given significance level (using the corrected pvalue field)Map<Long,Map<Long,DiffExprGeneSearchResult>>
findDiffExAnalysisResultIdsInResultSets(Collection<DiffExResultSetSummaryValueObject> resultSets, Collection<Long> geneIds)
List<DifferentialExpressionValueObject>
findInResultSet(ExpressionAnalysisResultSet resultSet, Double threshold, int maxResultsToReturn, int minNumberOfResults)
Map<Long,ContrastsValueObject>
loadContrastDetailsForResults(Collection<Long> ids)
Histogram
loadPvalueDistribution(Long resultSetId)
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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
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Method Detail
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findByGeneAndExperimentAnalyzed
Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>> findByGeneAndExperimentAnalyzed(Gene gene, Collection<Long> experimentsAnalyzed, double threshold, int limit)
Find differential expression for a gene in given data sets, exceeding a given significance level (using the corrected pvalue field)
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findByExperimentAnalyzed
Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>> findByExperimentAnalyzed(Collection<Long> experimentsAnalyzed, 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
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findByGene
Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>> findByGene(Gene gene)
Find differential expression results for a given gene, grouped by experiment.- Returns:
- a map of a collection of
DifferentialExpressionAnalysisResult
s keyed byBioAssaySet
.
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findByGeneAndExperimentAnalyzed
Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>> findByGeneAndExperimentAnalyzed(Gene gene, Collection<Long> experimentsAnalyzed)
Find differential expression results for a given gene and set of experiments, grouped by experiment.- Returns:
- a map of a collection of
DifferentialExpressionAnalysisResult
s keyed byBioAssaySet
.
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findDiffExAnalysisResultIdsInResultSets
Map<Long,Map<Long,DiffExprGeneSearchResult>> findDiffExAnalysisResultIdsInResultSets(Collection<DiffExResultSetSummaryValueObject> resultSets, Collection<Long> geneIds)
- Returns:
- map of resultSetId to map of gene to DiffExprGeneSearchResult
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findInResultSet
List<DifferentialExpressionValueObject> findInResultSet(ExpressionAnalysisResultSet resultSet, Double threshold, int maxResultsToReturn, int minNumberOfResults)
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loadContrastDetailsForResults
Map<Long,ContrastsValueObject> loadContrastDetailsForResults(Collection<Long> ids)
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find
Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>> find(Gene gene, double threshold, int limit)
Find differential expression for a gene, exceeding a given significance level (using the corrected pvalue field)- Parameters:
gene
- genethreshold
- thresholdlimit
- limit- Returns:
- map to diff exp VOs
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