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

Interface DifferentialExpressionResultDao

All Superinterfaces:

BaseDao<DifferentialExpressionAnalysisResult>

All Known Implementing Classes:

DifferentialExpressionResultDaoImpl

public interface DifferentialExpressionResultDao
extends BaseDao<DifferentialExpressionAnalysisResult>

See Also:

DifferentialExpressionAnalysisResult

Method Summary

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 experiments
Map<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, Map<DifferentialExpressionAnalysisResult,Baseline> baselineMap, double threshold, boolean keepNonSpecificProbes, boolean initializeFactorValues)	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,
                                                                           @Nullable
                                                                           Map<DifferentialExpressionAnalysisResult,Baseline> baselineMap,
                                                                           double threshold,
                                                                           boolean keepNonSpecificProbes,
                                                                           boolean initializeFactorValues)

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 for

experimentAnalyzedIds - list of IDs of experiments or experiment subsets to consider

includeSubsets - include results from experiment subsets

sourceExperimentIdMap - a mapping of results to source experiment ID

experimentAnalyzedIdMap - a mapping of results to experiment analyzed ID

baselineMap - a mapping of results to baselines

threshold - a maximum threshold on the corrected P-value, between 0 and 1 inclusively

keepNonSpecificProbes - whether to keep probes that map to more than one gene

initializeFactorValues - whether to initialize factor values in contrasts and baselines, note that their experimental factors will not be initialized

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 DifferentialExpressionAnalysisResults keyed by BioAssaySet.

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 DifferentialExpressionAnalysisResults keyed by BioAssaySet.

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 - gene

threshold - threshold

limit - limit

Returns:

map to diff exp VOs

loadPvalueDistribution

Histogram loadPvalueDistribution(Long resultSetId)