Uses of Class
ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResult

Packages that use DifferentialExpressionAnalysisResult

Package	Description
ubic.gemma.core.analysis.service
ubic.gemma.model.analysis.expression.diff
ubic.gemma.persistence.service.analysis.expression.diff
ubic.gemma.persistence.util
ubic.gemma.rest

Uses of DifferentialExpressionAnalysisResult in ubic.gemma.core.analysis.service

Method parameters in ubic.gemma.core.analysis.service with type arguments of type DifferentialExpressionAnalysisResult

Modifier and Type	Method	Description
void	DifferentialExpressionAnalysisResultListFileService.writeTsv(List<DifferentialExpressionAnalysisResult> payload, Gene gene, Map<DifferentialExpressionAnalysisResult, Long> sourceExperimentIdMap, Map<DifferentialExpressionAnalysisResult, Long> experimentAnalyzedIdMap, Map<DifferentialExpressionAnalysisResult, Baseline> baselineMap, Writer writer)	Writes a list of DE results with additional columns for mapping them to source experiments and analyzed experiments (for subsets).
void	DifferentialExpressionAnalysisResultListFileService.writeTsv(List<DifferentialExpressionAnalysisResult> payload, Gene gene, Map<DifferentialExpressionAnalysisResult, Long> sourceExperimentIdMap, Map<DifferentialExpressionAnalysisResult, Long> experimentAnalyzedIdMap, Map<DifferentialExpressionAnalysisResult, Baseline> baselineMap, Writer writer)	Writes a list of DE results with additional columns for mapping them to source experiments and analyzed experiments (for subsets).
void	DifferentialExpressionAnalysisResultListFileServiceImpl.writeTsv(List<DifferentialExpressionAnalysisResult> entity, Gene gene, Map<DifferentialExpressionAnalysisResult, Long> sourceExperimentIdMap, Map<DifferentialExpressionAnalysisResult, Long> experimentAnalyzedIdMap, Map<DifferentialExpressionAnalysisResult, Baseline> baselineMap, Writer writer)
void	DifferentialExpressionAnalysisResultListFileServiceImpl.writeTsv(List<DifferentialExpressionAnalysisResult> entity, Gene gene, Map<DifferentialExpressionAnalysisResult, Long> sourceExperimentIdMap, Map<DifferentialExpressionAnalysisResult, Long> experimentAnalyzedIdMap, Map<DifferentialExpressionAnalysisResult, Baseline> baselineMap, Writer writer)

Uses of DifferentialExpressionAnalysisResult in ubic.gemma.model.analysis.expression.diff

Subclasses with type arguments of type DifferentialExpressionAnalysisResult in ubic.gemma.model.analysis.expression.diff

Modifier and Type	Class	Description
class	DifferentialExpressionAnalysisResultSetValueObject	Wraps an ExpressionAnalysisResultSet and expose it to the public API.
class	DifferentialExpressionAnalysisResultValueObject	Unlike DiffExResultSetSummaryValueObject, this value object is meant for the public API.
class	ExpressionAnalysisResultSet	A group of results for an ExpressionExperiment.

Methods in ubic.gemma.model.analysis.expression.diff that return DifferentialExpressionAnalysisResult

Modifier and Type	Method	Description
static DifferentialExpressionAnalysisResult	DifferentialExpressionAnalysisResult.Factory.newInstance()

Methods in ubic.gemma.model.analysis.expression.diff that return types with arguments of type DifferentialExpressionAnalysisResult

Modifier and Type	Method	Description
Set<DifferentialExpressionAnalysisResult>	ExpressionAnalysisResultSet.getResults()
Set<DifferentialExpressionAnalysisResult>	GeneDifferentialExpressionMetaAnalysisResult.getResultsUsed()

Method parameters in ubic.gemma.model.analysis.expression.diff with type arguments of type DifferentialExpressionAnalysisResult

Modifier and Type	Method	Description
void	ExpressionAnalysisResultSet.setResults(Set<DifferentialExpressionAnalysisResult> results)
void	GeneDifferentialExpressionMetaAnalysisResult.setResultsUsed(Set<DifferentialExpressionAnalysisResult> resultsUsed)

Constructors in ubic.gemma.model.analysis.expression.diff with parameters of type DifferentialExpressionAnalysisResult

Modifier	Constructor	Description
	ContrastsValueObject(DifferentialExpressionAnalysisResult o)
	DifferentialExpressionAnalysisResultValueObject(DifferentialExpressionAnalysisResult result, boolean includeFactorValues)
	DifferentialExpressionAnalysisResultValueObject(DifferentialExpressionAnalysisResult result, boolean includeFactorValuesInContrasts, Set<Gene> genes, boolean includeTaxonInGenes)
	DifferentialExpressionValueObject(DifferentialExpressionAnalysisResult o)

Uses of DifferentialExpressionAnalysisResult in ubic.gemma.persistence.service.analysis.expression.diff

Subclasses with type arguments of type DifferentialExpressionAnalysisResult in ubic.gemma.persistence.service.analysis.expression.diff

Modifier and Type	Class	Description
class	DifferentialExpressionResultDaoImpl	This is a key class for queries to retrieve differential expression results (as well as standard CRUD aspects of working with DifferentialExpressionResults).
class	DifferentialExpressionResultServiceImpl	Facade for DifferentialExpressionResultService.

Subinterfaces with type arguments of type DifferentialExpressionAnalysisResult in ubic.gemma.persistence.service.analysis.expression.diff

Modifier and Type	Interface	Description
interface	DifferentialExpressionResultDao
interface	DifferentialExpressionResultService	Main entry point to retrieve differential expression data.
interface	ExpressionAnalysisResultSetDao
interface	ExpressionAnalysisResultSetService	🔒 The loaders below are ACL-guarded.

Methods in ubic.gemma.persistence.service.analysis.expression.diff that return types with arguments of type DifferentialExpressionAnalysisResult

Modifier and Type	Method	Description
Collection<DifferentialExpressionAnalysisResult>	DifferentialExpressionResultDaoImpl.create(Collection<DifferentialExpressionAnalysisResult> entities)
Map<BioAssaySet, List<DifferentialExpressionAnalysisResult>>	DifferentialExpressionResultDao.findByExperimentAnalyzed(Collection<Long> experimentAnalyzedIds, 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<BioAssaySet, List<DifferentialExpressionAnalysisResult>>	DifferentialExpressionResultDaoImpl.findByExperimentAnalyzed(Collection<Long> experimentAnalyzedIds, boolean includeSubSets, double threshold, int limit)
Map<BioAssaySet, List<DifferentialExpressionAnalysisResult>>	DifferentialExpressionResultDao.findByGene(Gene gene, boolean useGene2Cs, boolean keepNonSpecificProbes)	Find differential expression results for a given gene, grouped by experiment.
Map<BioAssaySet, List<DifferentialExpressionAnalysisResult>>	DifferentialExpressionResultDao.findByGene(Gene gene, boolean useGene2Cs, boolean keepNonSpecificProbes, double threshold, int limit)	Find differential expression for a gene, exceeding a given significance level (using the corrected pvalue field)
Map<BioAssaySet, List<DifferentialExpressionAnalysisResult>>	DifferentialExpressionResultDaoImpl.findByGene(Gene gene, boolean useGene2Cs, boolean keepNonSpecificProbes)
Map<BioAssaySet, List<DifferentialExpressionAnalysisResult>>	DifferentialExpressionResultDaoImpl.findByGene(Gene gene, boolean useGene2Cs, boolean keepNonSpecificProbes, double threshold, int limit)
Map<BioAssaySet, List<DifferentialExpressionAnalysisResult>>	DifferentialExpressionResultDao.findByGeneAndExperimentAnalyzed(Gene gene, boolean useGene2Cs, boolean keepNonSpecificProbes, Collection<Long> experimentAnalyzedIds, boolean includeSubSets)	Find differential expression results for a given gene and set of experiments, grouped by experiment.
Map<BioAssaySet, List<DifferentialExpressionAnalysisResult>>	DifferentialExpressionResultDao.findByGeneAndExperimentAnalyzed(Gene gene, boolean useGene2Cs, boolean keepNonSpecificProbes, Collection<Long> 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>	DifferentialExpressionResultDao.findByGeneAndExperimentAnalyzed(Gene gene, Collection<Long> experimentAnalyzedIds, boolean includeSubsets, Map<DifferentialExpressionAnalysisResult, Long> sourceExperimentIdMap, Map<DifferentialExpressionAnalysisResult, Long> experimentAnalyzedIdMap, Map<DifferentialExpressionAnalysisResult, Baseline> baselineMap, double threshold, boolean useGene2Cs, boolean keepNonSpecificProbes, boolean initializeFactorValues)	Retrieve differential expression results for a given gene across all the given datasets.
Map<BioAssaySet, List<DifferentialExpressionAnalysisResult>>	DifferentialExpressionResultDaoImpl.findByGeneAndExperimentAnalyzed(Gene gene, boolean useGene2Cs, boolean keepNonSpecificProbes, Collection<Long> experimentAnalyzedIds, boolean includeSubSets)
Map<BioAssaySet, List<DifferentialExpressionAnalysisResult>>	DifferentialExpressionResultDaoImpl.findByGeneAndExperimentAnalyzed(Gene gene, boolean useGene2Cs, boolean keepNonSpecificProbes, Collection<Long> experimentAnalyzedIds, boolean includeSubsets, double threshold, int limit)
List<DifferentialExpressionAnalysisResult>	DifferentialExpressionResultDaoImpl.findByGeneAndExperimentAnalyzed(Gene gene, Collection<Long> experimentAnalyzedIds, boolean includeSubsets, Map<DifferentialExpressionAnalysisResult, Long> sourceExperimentIdMap, Map<DifferentialExpressionAnalysisResult, Long> experimentAnalyzedIdMap, Map<DifferentialExpressionAnalysisResult, Baseline> baselineMap, double threshold, boolean useGene2Cs, boolean keepNonSpecificProbes, boolean initializeFactorValues)
List<DifferentialExpressionAnalysisResult>	DifferentialExpressionResultReadService.findByGeneAndExperimentAnalyzedIds(Gene gene, boolean useGene2Cs, boolean keepNonSpecific, Collection<Long> experimentAnalyzedIds, boolean includeSubSets, Map<DifferentialExpressionAnalysisResult, Long> sourceExperimentIdMap, Map<DifferentialExpressionAnalysisResult, Long> experimentAnalyzedIdMap, Map<DifferentialExpressionAnalysisResult, Baseline> baselineMap, double threshold, boolean initializeFactorValues)
List<DifferentialExpressionAnalysisResult>	DifferentialExpressionResultReadServiceImpl.findByGeneAndExperimentAnalyzedIds(Gene gene, boolean useGene2Cs, boolean keepNonSpecific, Collection<Long> experimentAnalyzedIds, boolean includeSubSets, Map<DifferentialExpressionAnalysisResult, Long> sourceExperimentIdMap, Map<DifferentialExpressionAnalysisResult, Long> experimentAnalyzedIdMap, Map<DifferentialExpressionAnalysisResult, Baseline> baselineMap, double threshold, boolean initializeFactorValues)
List<DifferentialExpressionAnalysisResult>	DifferentialExpressionResultService.findByGeneAndExperimentAnalyzedIds(Gene gene, boolean useGene2Cs, boolean keepNonSpecific, Collection<Long> experimentAnalyzedIds, boolean includeSubSets, Map<DifferentialExpressionAnalysisResult, Long> sourceExperimentIdMap, Map<DifferentialExpressionAnalysisResult, Long> experimentAnalyzedIdMap, Map<DifferentialExpressionAnalysisResult, Baseline> baselineMap, double threshold, boolean initializeFactorValues)
List<DifferentialExpressionAnalysisResult>	DifferentialExpressionResultServiceImpl.findByGeneAndExperimentAnalyzedIds(Gene gene, boolean useGene2Cs, boolean keepNonSpecific, Collection<Long> experimentAnalyzedIds, boolean includeSubSets, Map<DifferentialExpressionAnalysisResult, Long> sourceExperimentIdMap, Map<DifferentialExpressionAnalysisResult, Long> experimentAnalyzedIdMap, Map<DifferentialExpressionAnalysisResult, Baseline> baselineMap, double threshold, boolean initializeFactorValues)
Collection<DifferentialExpressionAnalysisResult>	DifferentialExpressionResultDaoImpl.loadAll()

Methods in ubic.gemma.persistence.service.analysis.expression.diff with parameters of type DifferentialExpressionAnalysisResult

Modifier and Type	Method	Description
void	DifferentialExpressionResultDaoImpl.remove(DifferentialExpressionAnalysisResult entity)

Method parameters in ubic.gemma.persistence.service.analysis.expression.diff with type arguments of type DifferentialExpressionAnalysisResult

Modifier and Type	Method	Description
Collection<DifferentialExpressionAnalysisResult>	DifferentialExpressionResultDaoImpl.create(Collection<DifferentialExpressionAnalysisResult> entities)
List<DifferentialExpressionAnalysisResult>	DifferentialExpressionResultDao.findByGeneAndExperimentAnalyzed(Gene gene, Collection<Long> experimentAnalyzedIds, boolean includeSubsets, Map<DifferentialExpressionAnalysisResult, Long> sourceExperimentIdMap, Map<DifferentialExpressionAnalysisResult, Long> experimentAnalyzedIdMap, Map<DifferentialExpressionAnalysisResult, Baseline> baselineMap, double threshold, boolean useGene2Cs, boolean keepNonSpecificProbes, boolean initializeFactorValues)	Retrieve differential expression results for a given gene across all the given datasets.
List<DifferentialExpressionAnalysisResult>	DifferentialExpressionResultDaoImpl.findByGeneAndExperimentAnalyzed(Gene gene, Collection<Long> experimentAnalyzedIds, boolean includeSubsets, Map<DifferentialExpressionAnalysisResult, Long> sourceExperimentIdMap, Map<DifferentialExpressionAnalysisResult, Long> experimentAnalyzedIdMap, Map<DifferentialExpressionAnalysisResult, Baseline> baselineMap, double threshold, boolean useGene2Cs, boolean keepNonSpecificProbes, boolean initializeFactorValues)
List<DifferentialExpressionAnalysisResult>	DifferentialExpressionResultReadService.findByGeneAndExperimentAnalyzedIds(Gene gene, boolean useGene2Cs, boolean keepNonSpecific, Collection<Long> experimentAnalyzedIds, boolean includeSubSets, Map<DifferentialExpressionAnalysisResult, Long> sourceExperimentIdMap, Map<DifferentialExpressionAnalysisResult, Long> experimentAnalyzedIdMap, Map<DifferentialExpressionAnalysisResult, Baseline> baselineMap, double threshold, boolean initializeFactorValues)
List<DifferentialExpressionAnalysisResult>	DifferentialExpressionResultReadServiceImpl.findByGeneAndExperimentAnalyzedIds(Gene gene, boolean useGene2Cs, boolean keepNonSpecific, Collection<Long> experimentAnalyzedIds, boolean includeSubSets, Map<DifferentialExpressionAnalysisResult, Long> sourceExperimentIdMap, Map<DifferentialExpressionAnalysisResult, Long> experimentAnalyzedIdMap, Map<DifferentialExpressionAnalysisResult, Baseline> baselineMap, double threshold, boolean initializeFactorValues)
List<DifferentialExpressionAnalysisResult>	DifferentialExpressionResultService.findByGeneAndExperimentAnalyzedIds(Gene gene, boolean useGene2Cs, boolean keepNonSpecific, Collection<Long> experimentAnalyzedIds, boolean includeSubSets, Map<DifferentialExpressionAnalysisResult, Long> sourceExperimentIdMap, Map<DifferentialExpressionAnalysisResult, Long> experimentAnalyzedIdMap, Map<DifferentialExpressionAnalysisResult, Baseline> baselineMap, double threshold, boolean initializeFactorValues)
List<DifferentialExpressionAnalysisResult>	DifferentialExpressionResultServiceImpl.findByGeneAndExperimentAnalyzedIds(Gene gene, boolean useGene2Cs, boolean keepNonSpecific, Collection<Long> experimentAnalyzedIds, boolean includeSubSets, Map<DifferentialExpressionAnalysisResult, Long> sourceExperimentIdMap, Map<DifferentialExpressionAnalysisResult, Long> experimentAnalyzedIdMap, Map<DifferentialExpressionAnalysisResult, Baseline> baselineMap, double threshold, boolean initializeFactorValues)

Uses of DifferentialExpressionAnalysisResult in ubic.gemma.persistence.util

Classes in ubic.gemma.persistence.util that implement interfaces with type arguments of type DifferentialExpressionAnalysisResult

Modifier and Type	Class	Description
class	DifferentialExpressionAnalysisResultComparator

Methods in ubic.gemma.persistence.util with parameters of type DifferentialExpressionAnalysisResult

Modifier and Type	Method	Description
int	DifferentialExpressionAnalysisResultComparator.compare(DifferentialExpressionAnalysisResult ear1, DifferentialExpressionAnalysisResult ear2)

Uses of DifferentialExpressionAnalysisResult in ubic.gemma.rest

Constructors in ubic.gemma.rest with parameters of type DifferentialExpressionAnalysisResult

Modifier	Constructor	Description
	DifferentialExpressionAnalysisResultByGeneValueObject(DifferentialExpressionAnalysisResult result, Long sourceExperimentId, Long experimentAnalyzedId, Baseline baseline)