Interface DifferentialExpressionResultDao
-
- All Superinterfaces:
BaseDao<DifferentialExpressionAnalysisResult>
- All Known Implementing Classes:
DifferentialExpressionResultDaoImpl
public interface DifferentialExpressionResultDao extends BaseDao<DifferentialExpressionAnalysisResult>
- See Also:
DifferentialExpressionAnalysisResult
-
-
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.List<DifferentialExpressionAnalysisResult>
findByGeneAndExperimentAnalyzed(Gene gene, Collection<Long> experimentAnalyzedIds, boolean includeSubsets, Map<DifferentialExpressionAnalysisResult,Long> sourceExperimentIdMap, Map<DifferentialExpressionAnalysisResult,Long> experimentAnalyzedIdMap, double threshold, boolean keepNonSpecificProbes)
Retrieve differential expression results for a given gene across all the given datasets.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)
-
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
-
-
-
-
Method Detail
-
findByGeneAndExperimentAnalyzed
List<DifferentialExpressionAnalysisResult> findByGeneAndExperimentAnalyzed(Gene gene, Collection<Long> experimentAnalyzedIds, boolean includeSubsets, @Nullable Map<DifferentialExpressionAnalysisResult,Long> sourceExperimentIdMap, @Nullable Map<DifferentialExpressionAnalysisResult,Long> experimentAnalyzedIdMap, double threshold, boolean keepNonSpecificProbes)
Retrieve differential expression results for a given gene across all the given datasets.Results are grouped by result set. If a gene maps to more than one probe, the result with the lowest corrected P-value is selected.
- Parameters:
gene
- a specific gene to retrieve differential expression forexperimentAnalyzedIds
- list of IDs of experiments or experiment subsets to considerincludeSubsets
- include results from experiment subsetssourceExperimentIdMap
- a mapping of results to source experiment IDexperimentAnalyzedIdMap
- a mapping of results to experiment analyzed IDthreshold
- a maximum threshold on the corrected P-value, between 0 and 1 inclusivelykeepNonSpecificProbes
- whether to keep probes that map to more than one gene- Returns:
- differential expression results, grouped by analyzed experiment ID
-
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)
-
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
-
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
.
-
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
.
-
findDiffExAnalysisResultIdsInResultSets
Map<Long,Map<Long,DiffExprGeneSearchResult>> findDiffExAnalysisResultIdsInResultSets(Collection<DiffExResultSetSummaryValueObject> resultSets, Collection<Long> geneIds)
- Returns:
- map of resultSetId to map of gene to DiffExprGeneSearchResult
-
findInResultSet
List<DifferentialExpressionValueObject> findInResultSet(ExpressionAnalysisResultSet resultSet, Double threshold, int maxResultsToReturn, int minNumberOfResults)
-
loadContrastDetailsForResults
Map<Long,ContrastsValueObject> loadContrastDetailsForResults(Collection<Long> ids)
-
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
-
-