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

Packages that use ExpressionAnalysisResultSet

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

Uses of ExpressionAnalysisResultSet in ubic.gemma.core.analysis.expression.diff

Methods in ubic.gemma.core.analysis.expression.diff that return types with arguments of type ExpressionAnalysisResultSet

Modifier and Type	Method	Description
Collection<ExpressionAnalysisResultSet>	DifferentialExpressionAnalyzerService.extendAnalysis(ExpressionExperiment ee, DifferentialExpressionAnalysis toUpdate)	Like redo, but we don't save the results, we just add the full set of results to the analysis given.
Collection<ExpressionAnalysisResultSet>	DifferentialExpressionAnalyzerServiceImpl.extendAnalysis(ExpressionExperiment ee, DifferentialExpressionAnalysis toUpdate)

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

Methods in ubic.gemma.core.analysis.service with parameters of type ExpressionAnalysisResultSet

Modifier and Type	Method	Description
List<DifferentialExpressionAnalysisResult>	ExpressionDataFileService.analysisResultSetToString(ExpressionAnalysisResultSet ears, Map<Long,String[]> geneAnnotations, StringBuilder buf, Map<Long,StringBuilder> probe2String, List<DifferentialExpressionAnalysisResult> sortedFirstColumnOfResults)
List<DifferentialExpressionAnalysisResult>	ExpressionDataFileServiceImpl.analysisResultSetToString(ExpressionAnalysisResultSet ears, Map<Long,String[]> geneAnnotations, StringBuilder buf, Map<Long,StringBuilder> probe2String, List<DifferentialExpressionAnalysisResult> sortedFirstColumnOfResults)
void	ExpressionAnalysisResultSetFileService.writeTsv(ExpressionAnalysisResultSet entity, Writer writer)	Write the analysis result set to an Appendable using a tabular format.
void	ExpressionAnalysisResultSetFileService.writeTsv(ExpressionAnalysisResultSet analysisResultSet, Baseline baseline, Map<Long,List<Gene>> result2Genes, Writer writer)	Write the analysis result set with result-to-gene mappings.
void	ExpressionAnalysisResultSetFileServiceImpl.writeTsv(ExpressionAnalysisResultSet entity, Writer writer)
void	ExpressionAnalysisResultSetFileServiceImpl.writeTsv(ExpressionAnalysisResultSet analysisResultSet, Baseline baseline, Map<Long,List<Gene>> resultId2Genes, Writer appendable)

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

Modifier and Type	Method	Description
void	ExpressionDataFileService.analysisResultSetsToString(Collection<ExpressionAnalysisResultSet> results, Map<Long,String[]> geneAnnotations, StringBuilder buf)
void	ExpressionDataFileServiceImpl.analysisResultSetsToString(Collection<ExpressionAnalysisResultSet> results, Map<Long,String[]> geneAnnotations, StringBuilder buf)

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

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

Modifier and Type	Method	Description
ExpressionAnalysisResultSet	DifferentialExpressionAnalysisResult.getResultSet()
static ExpressionAnalysisResultSet	ExpressionAnalysisResultSet.Factory.newInstance()
static ExpressionAnalysisResultSet	ExpressionAnalysisResultSet.Factory.newInstance(Set<ExperimentalFactor> experimentalFactors, Integer numberOfProbesTested, Integer numberOfGenesTested, FactorValue baselineGroup, Set<DifferentialExpressionAnalysisResult> results, DifferentialExpressionAnalysis analysis, PvalueDistribution pvalueDistribution, Set<HitListSize> hitListSizes)

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

Modifier and Type	Method	Description
Set<ExpressionAnalysisResultSet>	DifferentialExpressionAnalysis.getResultSets()	Groups of results produced by this differential expression analysis.
Set<ExpressionAnalysisResultSet>	GeneDifferentialExpressionMetaAnalysis.getResultSetsIncluded()

Methods in ubic.gemma.model.analysis.expression.diff with parameters of type ExpressionAnalysisResultSet

Modifier and Type	Method	Description
void	DifferentialExpressionAnalysisResult.setResultSet(ExpressionAnalysisResultSet resultSet)

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

Modifier and Type	Method	Description
void	DifferentialExpressionAnalysis.setResultSets(Set<ExpressionAnalysisResultSet> resultSets)
void	GeneDifferentialExpressionMetaAnalysis.setResultSetsIncluded(Set<ExpressionAnalysisResultSet> resultSetsIncluded)

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

Constructor	Description
DifferentialExpressionAnalysisResultSetValueObject(ExpressionAnalysisResultSet analysisResultSet)	Create a simple analysis results set VO with limited data.
DifferentialExpressionAnalysisResultSetValueObject(ExpressionAnalysisResultSet analysisResultSet, boolean includeFactorValuesInContrasts, Map<Long,List<Gene>> result2Genes, boolean includeTaxonInGenes)	Create an expression analysis result set VO with all its associated results.
DiffExResultSetSummaryValueObject(ExpressionAnalysisResultSet resultSet)

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

Methods in ubic.gemma.persistence.service.analysis.expression.diff that return ExpressionAnalysisResultSet

Modifier and Type	Method	Description
ExpressionAnalysisResultSet	ExpressionAnalysisResultSetDaoImpl.create(ExpressionAnalysisResultSet entity)
ExpressionAnalysisResultSet	ExpressionAnalysisResultSetService.loadWithAnalysis(Long id)
ExpressionAnalysisResultSet	ExpressionAnalysisResultSetServiceImpl.loadWithAnalysis(Long id)
ExpressionAnalysisResultSet	ExpressionAnalysisResultSetService.loadWithExperimentAnalyzed(Long id)
ExpressionAnalysisResultSet	ExpressionAnalysisResultSetServiceImpl.loadWithExperimentAnalyzed(Long id)
ExpressionAnalysisResultSet	ExpressionAnalysisResultSetDao.loadWithResultsAndContrasts(Long id)	Load an analysis result set with its all of its associated results.
ExpressionAnalysisResultSet	ExpressionAnalysisResultSetDao.loadWithResultsAndContrasts(Long id, double threshold, int offset, int limit)	Load a slice of an analysis result set with a corrected P-value threshold.
ExpressionAnalysisResultSet	ExpressionAnalysisResultSetDao.loadWithResultsAndContrasts(Long id, int offset, int limit)	Load a slice of an analysis result set.
ExpressionAnalysisResultSet	ExpressionAnalysisResultSetDaoImpl.loadWithResultsAndContrasts(Long id)
ExpressionAnalysisResultSet	ExpressionAnalysisResultSetDaoImpl.loadWithResultsAndContrasts(Long id, double threshold, int offset, int limit)
ExpressionAnalysisResultSet	ExpressionAnalysisResultSetDaoImpl.loadWithResultsAndContrasts(Long id, int offset, int limit)
ExpressionAnalysisResultSet	ExpressionAnalysisResultSetService.loadWithResultsAndContrasts(Long value)
ExpressionAnalysisResultSet	ExpressionAnalysisResultSetService.loadWithResultsAndContrasts(Long value, double threshold, int offset, int limit)
ExpressionAnalysisResultSet	ExpressionAnalysisResultSetService.loadWithResultsAndContrasts(Long value, int offset, int limit)
ExpressionAnalysisResultSet	ExpressionAnalysisResultSetServiceImpl.loadWithResultsAndContrasts(Long value)
ExpressionAnalysisResultSet	ExpressionAnalysisResultSetServiceImpl.loadWithResultsAndContrasts(Long value, double threshold, int offset, int limit)
ExpressionAnalysisResultSet	ExpressionAnalysisResultSetServiceImpl.loadWithResultsAndContrasts(Long value, int offset, int limit)
ExpressionAnalysisResultSet	ExpressionAnalysisResultSetService.thaw(ExpressionAnalysisResultSet e)
ExpressionAnalysisResultSet	ExpressionAnalysisResultSetServiceImpl.thaw(ExpressionAnalysisResultSet ears)

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

Modifier and Type	Method	Description
Map<ExpressionAnalysisResultSet,Baseline>	ExpressionAnalysisResultSetDao.getBaselinesForInteractions(Collection<ExpressionAnalysisResultSet> resultSets, boolean initializeFactorValues)	Retrieve baselines for all the given result sets representing factor interactions.
Map<ExpressionAnalysisResultSet,Baseline>	ExpressionAnalysisResultSetDaoImpl.getBaselinesForInteractions(Collection<ExpressionAnalysisResultSet> resultSets, boolean initializeFactorValues)
Map<ExpressionAnalysisResultSet,Baseline>	ExpressionAnalysisResultSetService.getBaselinesForInteractions(Set<ExpressionAnalysisResultSet> resultSets, boolean initializeFactorValues)
Map<ExpressionAnalysisResultSet,Baseline>	ExpressionAnalysisResultSetServiceImpl.getBaselinesForInteractions(Set<ExpressionAnalysisResultSet> resultSets, boolean initializeFactorValues)

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

Modifier and Type	Method	Description
void	DifferentialExpressionResultCache.addToTopHitsCache(ExpressionAnalysisResultSet resultSet, List<DifferentialExpressionValueObject> items)
void	DifferentialExpressionResultCacheImpl.addToTopHitsCache(ExpressionAnalysisResultSet resultSet, List<DifferentialExpressionValueObject> items)
long	ExpressionAnalysisResultSetDao.countResults(ExpressionAnalysisResultSet ears)	Count the number of results in a given result set.
long	ExpressionAnalysisResultSetDao.countResults(ExpressionAnalysisResultSet ears, double threshold)	Count the number of results in a given result set below a given corrected P-value threshold.
long	ExpressionAnalysisResultSetDaoImpl.countResults(ExpressionAnalysisResultSet ears)
long	ExpressionAnalysisResultSetDaoImpl.countResults(ExpressionAnalysisResultSet ears, double threshold)
long	ExpressionAnalysisResultSetService.countResults(ExpressionAnalysisResultSet ears)
long	ExpressionAnalysisResultSetService.countResults(ExpressionAnalysisResultSet ears, double threshold)
long	ExpressionAnalysisResultSetServiceImpl.countResults(ExpressionAnalysisResultSet ears)
long	ExpressionAnalysisResultSetServiceImpl.countResults(ExpressionAnalysisResultSet ears, double threshold)
ExpressionAnalysisResultSet	ExpressionAnalysisResultSetDaoImpl.create(ExpressionAnalysisResultSet entity)
protected DifferentialExpressionAnalysisResultSetValueObject	ExpressionAnalysisResultSetDaoImpl.doLoadValueObject(ExpressionAnalysisResultSet entity)
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalysisDao.find(Gene gene, ExpressionAnalysisResultSet resultSet, double threshold)
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalysisService.find(Gene gene, ExpressionAnalysisResultSet resultSet, double threshold)
Collection<DifferentialExpressionAnalysis>	DifferentialExpressionAnalysisServiceImpl.find(Gene gene, ExpressionAnalysisResultSet resultSet, double threshold)
List<DifferentialExpressionValueObject>	DifferentialExpressionResultDao.findInResultSet(ExpressionAnalysisResultSet resultSet, double threshold, int maxResultsToReturn, int minNumberOfResults)
List<DifferentialExpressionValueObject>	DifferentialExpressionResultDaoImpl.findInResultSet(ExpressionAnalysisResultSet resultSet, double threshold, int limit, int minNumberOfResults)
List<DifferentialExpressionValueObject>	DifferentialExpressionResultService.findInResultSet(ExpressionAnalysisResultSet ar, Double threshold, int maxResultsToReturn, int minNumberOfResults)
List<DifferentialExpressionValueObject>	DifferentialExpressionResultServiceImpl.findInResultSet(ExpressionAnalysisResultSet resultSet, Double threshold, int maxResultsToReturn, int minNumberOfResults)
Baseline	ExpressionAnalysisResultSetDao.getBaseline(ExpressionAnalysisResultSet ears)	Retrieve the baseline for the given result set.
Baseline	ExpressionAnalysisResultSetDaoImpl.getBaseline(ExpressionAnalysisResultSet ears)
Baseline	ExpressionAnalysisResultSetService.getBaseline(ExpressionAnalysisResultSet ears)
Baseline	ExpressionAnalysisResultSetServiceImpl.getBaseline(ExpressionAnalysisResultSet ears)
List<DifferentialExpressionValueObject>	DifferentialExpressionResultCache.getTopHits(ExpressionAnalysisResultSet resultSet)
List<DifferentialExpressionValueObject>	DifferentialExpressionResultCacheImpl.getTopHits(ExpressionAnalysisResultSet resultSet)
Histogram	ExpressionAnalysisResultSetDao.loadPvalueDistribution(ExpressionAnalysisResultSet resultSet)	Obtain a histogram of the P-value distribution for a given result set.
Histogram	ExpressionAnalysisResultSetDaoImpl.loadPvalueDistribution(ExpressionAnalysisResultSet resultSet)
Histogram	ExpressionAnalysisResultSetService.loadPvalueDistribution(ExpressionAnalysisResultSet resulSet)
Histogram	ExpressionAnalysisResultSetServiceImpl.loadPvalueDistribution(ExpressionAnalysisResultSet resultSet)
Map<Long,List<Gene>>	ExpressionAnalysisResultSetService.loadResultIdToGenesMap(ExpressionAnalysisResultSet ears)
Map<Long,List<Gene>>	ExpressionAnalysisResultSetServiceImpl.loadResultIdToGenesMap(ExpressionAnalysisResultSet resultSet)
Map<Long,List<Gene>>	ExpressionAnalysisResultSetDao.loadResultToGenesMap(ExpressionAnalysisResultSet resultSet, boolean queryByResult)	Load a DifferentialExpressionAnalysisResult to Gene multi-map.
Map<Long,List<Gene>>	ExpressionAnalysisResultSetDaoImpl.loadResultToGenesMap(ExpressionAnalysisResultSet resultSet, boolean queryByResult)
DifferentialExpressionAnalysisResultSetValueObject	ExpressionAnalysisResultSetDao.loadValueObjectWithResults(ExpressionAnalysisResultSet resultSet, boolean includeFactorValuesInContrasts, boolean queryGenesByResult, boolean includeTaxonInGenes)	Load an analysis result set with its all of its associated results.
DifferentialExpressionAnalysisResultSetValueObject	ExpressionAnalysisResultSetDaoImpl.loadValueObjectWithResults(ExpressionAnalysisResultSet entity, boolean includeFactorValuesInContrasts, boolean queryGenesByResult, boolean includeTaxonInGenes)
DifferentialExpressionAnalysisResultSetValueObject	ExpressionAnalysisResultSetService.loadValueObjectWithResults(ExpressionAnalysisResultSet ears, boolean includeFactorValuesInContrasts, boolean queryByResult, boolean includeTaxonInGenes)
DifferentialExpressionAnalysisResultSetValueObject	ExpressionAnalysisResultSetServiceImpl.loadValueObjectWithResults(ExpressionAnalysisResultSet ears, boolean includeFactorValuesInContrasts, boolean queryByResult, boolean includeTaxonInGenes)
void	ExpressionAnalysisResultSetDaoImpl.remove(ExpressionAnalysisResultSet entity)
void	ExpressionAnalysisResultSetDao.thaw(ExpressionAnalysisResultSet ears)	Initialize the analysis and subset factor vale.
void	ExpressionAnalysisResultSetDaoImpl.thaw(ExpressionAnalysisResultSet ears)
ExpressionAnalysisResultSet	ExpressionAnalysisResultSetService.thaw(ExpressionAnalysisResultSet e)
ExpressionAnalysisResultSet	ExpressionAnalysisResultSetServiceImpl.thaw(ExpressionAnalysisResultSet ears)

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

Modifier and Type	Method	Description
Map<ExpressionAnalysisResultSet,Baseline>	ExpressionAnalysisResultSetDao.getBaselinesForInteractions(Collection<ExpressionAnalysisResultSet> resultSets, boolean initializeFactorValues)	Retrieve baselines for all the given result sets representing factor interactions.
Map<ExpressionAnalysisResultSet,Baseline>	ExpressionAnalysisResultSetDaoImpl.getBaselinesForInteractions(Collection<ExpressionAnalysisResultSet> resultSets, boolean initializeFactorValues)
Map<ExpressionAnalysisResultSet,Baseline>	ExpressionAnalysisResultSetService.getBaselinesForInteractions(Set<ExpressionAnalysisResultSet> resultSets, boolean initializeFactorValues)
Map<ExpressionAnalysisResultSet,Baseline>	ExpressionAnalysisResultSetServiceImpl.getBaselinesForInteractions(Set<ExpressionAnalysisResultSet> resultSets, boolean initializeFactorValues)

Uses of ExpressionAnalysisResultSet in ubic.gemma.rest

Method parameters in ubic.gemma.rest with type arguments of type ExpressionAnalysisResultSet

Modifier and Type	Method	Description
ResponseDataObject<Long>	AnalysisResultSetsWebService.getNumberOfResultSets(FilterArg<ExpressionAnalysisResultSet> filter)
FilteredAndPaginatedResponseDataObject<DifferentialExpressionAnalysisResultSetValueObject>	AnalysisResultSetsWebService.getResultSets(DatasetArrayArg datasets, DatabaseEntryArrayArg databaseEntries, FilterArg<ExpressionAnalysisResultSet> filters, OffsetArg offset, LimitArg limit, SortArg<ExpressionAnalysisResultSet> sort)	Retrieve all AnalysisResultSet matching a set of criteria.
FilteredAndPaginatedResponseDataObject<DifferentialExpressionAnalysisResultSetValueObject>	AnalysisResultSetsWebService.getResultSets(DatasetArrayArg datasets, DatabaseEntryArrayArg databaseEntries, FilterArg<ExpressionAnalysisResultSet> filters, OffsetArg offset, LimitArg limit, SortArg<ExpressionAnalysisResultSet> sort)	Retrieve all AnalysisResultSet matching a set of criteria.

Uses of ExpressionAnalysisResultSet in ubic.gemma.rest.util.args

Methods in ubic.gemma.rest.util.args that return ExpressionAnalysisResultSet

Modifier and Type	Method	Description
ExpressionAnalysisResultSet	ExpressionAnalysisResultSetArgService.getEntityWithContrastsAndResults(ExpressionAnalysisResultSetArg analysisResultSet)
ExpressionAnalysisResultSet	ExpressionAnalysisResultSetArgService.getEntityWithContrastsAndResults(ExpressionAnalysisResultSetArg analysisResultSet, double threshold, int offset, int limit)
ExpressionAnalysisResultSet	ExpressionAnalysisResultSetArgService.getEntityWithContrastsAndResults(ExpressionAnalysisResultSetArg analysisResultSet, int offset, int limit)