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(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>>	find(Gene gene)
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>>	find(Gene gene, Collection<Long> experimentsAnalyzed)
Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>>	find(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<Double>	findGeneInResultSets(Gene gene, ExpressionAnalysisResultSet resultSet, Collection<Long> arrayDesignIds, int limit)
List<DifferentialExpressionValueObject>	findInResultSet(ExpressionAnalysisResultSet resultSet, Double threshold, int maxResultsToReturn, int minNumberOfResults)
Map<ExpressionAnalysisResultSet,List<DifferentialExpressionAnalysisResult>>	findInResultSets(Collection<ExpressionAnalysisResultSet> resultsAnalyzed, double threshold, int limit)	Given a list of result sets finds the diff expression results that met the given threshold
DifferentialExpressionAnalysis	getAnalysis(ExpressionAnalysisResultSet rs)
Map<DifferentialExpressionAnalysisResult,Collection<ExperimentalFactor>>	getExperimentalFactors(Collection<DifferentialExpressionAnalysisResult> differentialExpressionAnalysisResults)
Collection<ExperimentalFactor>	getExperimentalFactors(DifferentialExpressionAnalysisResult differentialExpressionAnalysisResult)
Map<Long,ContrastsValueObject>	loadContrastDetailsForResults(Collection<Long> ids)
Histogram	loadPvalueDistribution(Long resultSetId)
void	thaw(Collection<DifferentialExpressionAnalysisResult> results)
void	thaw(DifferentialExpressionAnalysisResult result)

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

find

Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>> find(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)

Parameters:

gene - gene

experimentsAnalyzed - ees

threshold - threshold

limit - limit

Returns:

map to diff exp VOs

find

Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>> find(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

Parameters:

experimentsAnalyzed - ees

threshold - threshold

limit - limit

Returns:

map to diff exp VOs

find

Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>> find(Gene gene)

Parameters:

gene - gene

Returns:

a map of a collection of DifferentialExpressionAnalysisResults keyed by BioAssaySet.

find

Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>> find(Gene gene,
                                                                                        Collection<Long> experimentsAnalyzed)

Parameters:

gene - gene

experimentsAnalyzed - ees

Returns:

a map of a collection of DifferentialExpressionAnalysisResults keyed by BioAssaySet.

findDiffExAnalysisResultIdsInResultSets

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

Parameters:

geneIds - gene ids

resultSets - result sets

Returns:

map of resultSetId to map of gene to DiffExprGeneSearchResult

findGeneInResultSets

List<Double> findGeneInResultSets(Gene gene,
                                  ExpressionAnalysisResultSet resultSet,
                                  Collection<Long> arrayDesignIds,
                                  int limit)

findInResultSet

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

findInResultSets

Map<ExpressionAnalysisResultSet,List<DifferentialExpressionAnalysisResult>> findInResultSets(Collection<ExpressionAnalysisResultSet> resultsAnalyzed,
                                                                                                   double threshold,
                                                                                                   int limit)

Given a list of result sets finds the diff expression results that met the given threshold

Parameters:

resultsAnalyzed - resultsAnalyzed

threshold - threshold

limit - limit

Returns:

map to diff exp VOs

getAnalysis

DifferentialExpressionAnalysis getAnalysis(ExpressionAnalysisResultSet rs)

getExperimentalFactors

Collection<ExperimentalFactor> getExperimentalFactors(DifferentialExpressionAnalysisResult differentialExpressionAnalysisResult)

getExperimentalFactors

Map<DifferentialExpressionAnalysisResult,Collection<ExperimentalFactor>> getExperimentalFactors(Collection<DifferentialExpressionAnalysisResult> differentialExpressionAnalysisResults)

loadContrastDetailsForResults

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

thaw

void thaw(Collection<DifferentialExpressionAnalysisResult> results)

thaw

void thaw(DifferentialExpressionAnalysisResult result)

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)