Uses of Class
ubic.gemma.model.expression.experiment.ExpressionExperimentSubSet

Packages that use ExpressionExperimentSubSet

Package	Description
ubic.gemma.apps	This package contains built-in Gemma CLI applications.
ubic.gemma.core.analysis.expression.diff
ubic.gemma.core.analysis.preprocess.batcheffects
ubic.gemma.core.analysis.singleCell.aggregate	This packge contains classes for splitting and aggregating single-cell data.
ubic.gemma.core.visualization
ubic.gemma.model.expression.experiment
ubic.gemma.persistence.service.expression.experiment
ubic.gemma.persistence.util
ubic.gemma.rest
ubic.gemma.rest.util.args

Uses of ExpressionExperimentSubSet in ubic.gemma.apps

Methods in ubic.gemma.apps with parameters of type ExpressionExperimentSubSet

Modifier and Type	Method	Description
protected void	ExpressionExperimentManipulatingCLI.processExpressionExperimentSubSet(ExpressionExperimentSubSet expressionExperimentSubSet)	Process an ExpressionExperimentSubSet.

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

Methods in ubic.gemma.core.analysis.expression.diff with parameters of type ExpressionExperimentSubSet

Modifier and Type	Method	Description
DifferentialExpressionAnalysis	DiffExAnalyzer.run(ExpressionExperimentSubSet subset, ExpressionDataDoubleMatrix dmatrix, DifferentialExpressionAnalysisConfig config)	Analyze a subset.
DifferentialExpressionAnalysis	LinearModelAnalyzer.run(ExpressionExperimentSubSet subset, ExpressionDataDoubleMatrix dmatrix, DifferentialExpressionAnalysisConfig config)

Method parameters in ubic.gemma.core.analysis.expression.diff with type arguments of type ExpressionExperimentSubSet

Modifier and Type	Method	Description
Collection<DifferentialExpressionAnalysis>	DiffExAnalyzer.run(ExpressionExperiment expressionExperiment, Map<FactorValue,ExpressionExperimentSubSet> subsets, ExpressionDataDoubleMatrix dmatrix, DifferentialExpressionAnalysisConfig config)	Analyze a dataset with a pre-existing subset structure.
Collection<DifferentialExpressionAnalysis>	LinearModelAnalyzer.run(ExpressionExperiment ee, Map<FactorValue,ExpressionExperimentSubSet> subsets, ExpressionDataDoubleMatrix dmatrix, DifferentialExpressionAnalysisConfig config)

Uses of ExpressionExperimentSubSet in ubic.gemma.core.analysis.preprocess.batcheffects

Methods in ubic.gemma.core.analysis.preprocess.batcheffects that return types with arguments of type ExpressionExperimentSubSet

Modifier and Type	Method	Description
Map<ExpressionExperimentSubSet,List<BatchConfound>>	ExpressionExperimentBatchInformationService.getSignificantBatchConfoundsForSubsets(ExpressionExperiment ee)	Obtain the significant batch confounds for a dataset subsets.
Map<ExpressionExperimentSubSet,List<BatchConfound>>	ExpressionExperimentBatchInformationServiceImpl.getSignificantBatchConfoundsForSubsets(ExpressionExperiment ee)

Uses of ExpressionExperimentSubSet in ubic.gemma.core.analysis.singleCell.aggregate

Methods in ubic.gemma.core.analysis.singleCell.aggregate that return types with arguments of type ExpressionExperimentSubSet

Modifier and Type	Method	Description
List<ExpressionExperimentSubSet>	SingleCellExpressionExperimentSplitService.split(ExpressionExperiment ee, CellLevelCharacteristics clc, ExperimentalFactor factor, Map<Characteristic,FactorValue> cellTypeMapping, SplitConfig config)	Split biomaterials and bioassays by the given CellLevelCharacteristics.
List<ExpressionExperimentSubSet>	SingleCellExpressionExperimentSplitServiceImpl.split(ExpressionExperiment ee, CellLevelCharacteristics clc, ExperimentalFactor factor, Map<Characteristic,FactorValue> mappedCellTypeFactors, SplitConfig config)
List<ExpressionExperimentSubSet>	SingleCellExpressionExperimentSplitService.splitByCellType(ExpressionExperiment ee, SplitConfig config)	Split a single-cell dataset by cell type.
List<ExpressionExperimentSubSet>	SingleCellExpressionExperimentSplitServiceImpl.splitByCellType(ExpressionExperiment ee, SplitConfig config)

Method parameters in ubic.gemma.core.analysis.singleCell.aggregate with type arguments of type ExpressionExperimentSubSet

Modifier and Type	Method	Description
static Map<Characteristic,FactorValue>	CellLevelCharacteristicsMappingUtils.createMappingBySubSetCharacteristics(CellLevelCharacteristics clc, ExperimentalFactor factor, Map<FactorValue,ExpressionExperimentSubSet> subsets)	Infer the mapping of cell type assignments to factor values using a subset structure.

Uses of ExpressionExperimentSubSet in ubic.gemma.core.visualization

Methods in ubic.gemma.core.visualization with parameters of type ExpressionExperimentSubSet

Modifier and Type	Method	Description
static ExpressionDataHeatmap	ExpressionDataHeatmap.fromDesignElements(ExpressionExperimentSubSet subSet, BioAssayDimension dimension, Slice<CompositeSequence> designElements, List<Gene> genes)	Create a heatmap for a subset using design elements.
static ExpressionDataHeatmap	ExpressionDataHeatmap.fromVectors(ExpressionExperimentSubSet subSet, BioAssayDimension dimension, Slice<? extends BulkExpressionDataVector> vectors, List<Gene> genes)	Create a heatmap for a subset.

Constructor parameters in ubic.gemma.core.visualization with type arguments of type ExpressionExperimentSubSet

Constructor	Description
SingleCellSparsityHeatmap(ExpressionExperiment expressionExperiment, SingleCellDimension singleCellDimension, BioAssayDimension dimension, Collection<ExpressionExperimentSubSet> subSets, Map<BioAssay,Long> designElementsPerSample, SingleCellSparsityHeatmap.SingleCellHeatmapType type)

Uses of ExpressionExperimentSubSet in ubic.gemma.model.expression.experiment

Methods in ubic.gemma.model.expression.experiment that return ExpressionExperimentSubSet

Modifier and Type	Method	Description
static ExpressionExperimentSubSet	ExpressionExperimentSubSet.Factory.newInstance(String name, ExpressionExperiment sourceExperiment)

Constructors in ubic.gemma.model.expression.experiment with parameters of type ExpressionExperimentSubSet

Constructor	Description
ExpressionExperimentSubsetValueObject(ExpressionExperimentSubSet ees)
ExpressionExperimentSubsetValueObject(ExpressionExperimentSubSet ees, Map<ArrayDesign,ArrayDesignValueObject> arrayDesignValueObjectsById, Map<BioAssay,BioAssay> bioAssay2SourceBioAssayMap, boolean includeAssays, boolean basic, boolean allFactorValues)

Uses of ExpressionExperimentSubSet in ubic.gemma.persistence.service.expression.experiment

Methods in ubic.gemma.persistence.service.expression.experiment that return ExpressionExperimentSubSet

Modifier and Type	Method	Description
ExpressionExperimentSubSet	ExpressionExperimentSubSetService.create(ExpressionExperimentSubSet expressionExperimentSubSet)
ExpressionExperimentSubSet	ExpressionExperimentSubSetDaoImpl.find(ExpressionExperimentSubSet entity)
ExpressionExperimentSubSet	ExpressionExperimentSubSetService.find(ExpressionExperimentSubSet entity)
ExpressionExperimentSubSet	ExpressionExperimentSubSetService.findOrCreate(ExpressionExperimentSubSet entity)
ExpressionExperimentSubSet	ExpressionExperimentDao.getSubSetById(ExpressionExperiment ee, Long subSetId)
ExpressionExperimentSubSet	ExpressionExperimentDaoImpl.getSubSetById(ExpressionExperiment ee, Long subSetId)
ExpressionExperimentSubSet	ExpressionExperimentService.getSubSetByIdWithCharacteristics(ExpressionExperiment ee, Long subSetId)
ExpressionExperimentSubSet	ExpressionExperimentServiceImpl.getSubSetByIdWithCharacteristics(ExpressionExperiment ee, Long subSetId)
ExpressionExperimentSubSet	ExpressionExperimentService.getSubSetByIdWithCharacteristicsAndBioAssays(ExpressionExperiment ee, Long subSetId)	Obtain a particular subset by ID.
ExpressionExperimentSubSet	ExpressionExperimentServiceImpl.getSubSetByIdWithCharacteristicsAndBioAssays(ExpressionExperiment ee, Long subSetId)
ExpressionExperimentSubSet	ExpressionExperimentSubSetService.load(Long id)
ExpressionExperimentSubSet	ExpressionExperimentSubSetDao.loadWithBioAssays(Long id)
ExpressionExperimentSubSet	ExpressionExperimentSubSetDaoImpl.loadWithBioAssays(Long id)
ExpressionExperimentSubSet	ExpressionExperimentSubSetService.loadWithBioAssays(Long id)
ExpressionExperimentSubSet	ExpressionExperimentSubSetServiceImpl.loadWithBioAssays(Long id)

Methods in ubic.gemma.persistence.service.expression.experiment that return types with arguments of type ExpressionExperimentSubSet

Modifier and Type	Method	Description
Collection<ExpressionExperimentSubSet>	ExpressionExperimentSubSetDao.findByBioAssayIn(Collection<BioAssay> bioAssays)
Collection<ExpressionExperimentSubSet>	ExpressionExperimentSubSetDaoImpl.findByBioAssayIn(Collection<BioAssay> bioAssays)
Collection<ExpressionExperimentSubSet>	ExpressionExperimentSubSetService.findByBioAssayIn(Collection<BioAssay> bioAssays)
Collection<ExpressionExperimentSubSet>	ExpressionExperimentSubSetServiceImpl.findByBioAssayIn(Collection<BioAssay> bioAssays)
Collection<ExpressionExperimentSubSet>	ExpressionExperimentDao.getSubSets(ExpressionExperiment expressionExperiment)
Collection<ExpressionExperimentSubSet>	ExpressionExperimentDao.getSubSets(ExpressionExperiment expressionExperiment, BioAssayDimension bad)
Collection<ExpressionExperimentSubSet>	ExpressionExperimentDaoImpl.getSubSets(ExpressionExperiment expressionExperiment)
Collection<ExpressionExperimentSubSet>	ExpressionExperimentDaoImpl.getSubSets(ExpressionExperiment expressionExperiment, BioAssayDimension bad)
Collection<ExpressionExperimentSubSet>	ExpressionExperimentService.getSubSets(ExpressionExperiment expressionExperiment, BioAssayDimension dimension)	Obtain the subsets for a particular dimension.
Collection<ExpressionExperimentSubSet>	ExpressionExperimentServiceImpl.getSubSets(ExpressionExperiment expressionExperiment, BioAssayDimension dimension)
Map<BioAssayDimension,Set<ExpressionExperimentSubSet>>	ExpressionExperimentDao.getSubSetsByDimension(ExpressionExperiment expressionExperiment)
Map<BioAssayDimension,Set<ExpressionExperimentSubSet>>	ExpressionExperimentDaoImpl.getSubSetsByDimension(ExpressionExperiment expressionExperiment)
Map<BioAssayDimension,Set<ExpressionExperimentSubSet>>	ExpressionExperimentService.getSubSetsByDimension(ExpressionExperiment expressionExperiment)	Obtain all the subsets organized by dimension for a given dataset.
Map<BioAssayDimension,Set<ExpressionExperimentSubSet>>	ExpressionExperimentServiceImpl.getSubSetsByDimension(ExpressionExperiment expressionExperiment)
Map<BioAssayDimension,Set<ExpressionExperimentSubSet>>	ExpressionExperimentService.getSubSetsByDimensionWithBioAssays(ExpressionExperiment expressionExperiment)	Obtain all the subsets organized by dimension for a given dataset.
Map<BioAssayDimension,Set<ExpressionExperimentSubSet>>	ExpressionExperimentServiceImpl.getSubSetsByDimensionWithBioAssays(ExpressionExperiment expressionExperiment)
Map<ExperimentalFactor,Map<FactorValue,ExpressionExperimentSubSet>>	ExpressionExperimentService.getSubSetsByFactorValue(ExpressionExperiment expressionExperiment, BioAssayDimension dimension)	Reconstitute the FV to subset mapping for a given experiment.
Map<FactorValue,ExpressionExperimentSubSet>	ExpressionExperimentService.getSubSetsByFactorValue(ExpressionExperiment expressionExperiment, ExperimentalFactor experimentalFactor, BioAssayDimension dimension)	Reconstitute the FV to subset mapping for a given experiment and factor.
Map<ExperimentalFactor,Map<FactorValue,ExpressionExperimentSubSet>>	ExpressionExperimentServiceImpl.getSubSetsByFactorValue(ExpressionExperiment expressionExperiment, BioAssayDimension dimension)
Map<FactorValue,ExpressionExperimentSubSet>	ExpressionExperimentServiceImpl.getSubSetsByFactorValue(ExpressionExperiment expressionExperiment, ExperimentalFactor experimentalFactor, BioAssayDimension dimension)
Map<FactorValue,ExpressionExperimentSubSet>	ExpressionExperimentService.getSubSetsByFactorValueWithCharacteristicsAndBioAssays(ExpressionExperiment expressionExperiment, ExperimentalFactor experimentalFactor, BioAssayDimension dimension)	Reconstitute the FV to subset mapping for a given experiment and factor.
Map<FactorValue,ExpressionExperimentSubSet>	ExpressionExperimentServiceImpl.getSubSetsByFactorValueWithCharacteristicsAndBioAssays(ExpressionExperiment expressionExperiment, ExperimentalFactor experimentalFactor, BioAssayDimension dimension)
Collection<ExpressionExperimentSubSet>	ExpressionExperimentService.getSubSetsWithBioAssays(ExpressionExperiment expressionExperiment)	Obtain all the subsets for a given dataset.
Collection<ExpressionExperimentSubSet>	ExpressionExperimentService.getSubSetsWithBioAssays(ExpressionExperiment expressionExperiment, BioAssayDimension dimension)	Obtain the subsets for a particular dimension.
Collection<ExpressionExperimentSubSet>	ExpressionExperimentServiceImpl.getSubSetsWithBioAssays(ExpressionExperiment expressionExperiment)
Collection<ExpressionExperimentSubSet>	ExpressionExperimentServiceImpl.getSubSetsWithBioAssays(ExpressionExperiment expressionExperiment, BioAssayDimension dimension)
Collection<ExpressionExperimentSubSet>	ExpressionExperimentService.getSubSetsWithCharacteristics(ExpressionExperiment ee)	Obtain all the subsets for a given dataset.
Collection<ExpressionExperimentSubSet>	ExpressionExperimentServiceImpl.getSubSetsWithCharacteristics(ExpressionExperiment ee)
Collection<ExpressionExperimentSubSet>	ExpressionExperimentSubSetService.loadAll()

Methods in ubic.gemma.persistence.service.expression.experiment with parameters of type ExpressionExperimentSubSet

Modifier and Type	Method	Description
ExpressionExperimentSubSet	ExpressionExperimentSubSetService.create(ExpressionExperimentSubSet expressionExperimentSubSet)
ExpressionExperimentSubSet	ExpressionExperimentSubSetDaoImpl.find(ExpressionExperimentSubSet entity)
ExpressionExperimentSubSet	ExpressionExperimentSubSetService.find(ExpressionExperimentSubSet entity)
ExpressionExperimentSubSet	ExpressionExperimentSubSetService.findOrCreate(ExpressionExperimentSubSet entity)
Set<AnnotationValueObject>	ExpressionExperimentService.getAnnotations(ExpressionExperimentSubSet ee)	Retrieve annotations for a given experiment subset.
Set<AnnotationValueObject>	ExpressionExperimentServiceImpl.getAnnotations(ExpressionExperimentSubSet ee)
List<Characteristic>	ExpressionExperimentDao.getBioMaterialAnnotations(ExpressionExperimentSubSet expressionExperiment)
List<Characteristic>	ExpressionExperimentDaoImpl.getBioMaterialAnnotations(ExpressionExperimentSubSet subset)
List<Statement>	ExpressionExperimentDao.getFactorValueAnnotations(ExpressionExperimentSubSet ee)	Obtain factor value-level annotations for a given subset.
List<Statement>	ExpressionExperimentDaoImpl.getFactorValueAnnotations(ExpressionExperimentSubSet subset)
Collection<FactorValue>	ExpressionExperimentSubSetDao.getFactorValuesUsed(ExpressionExperimentSubSet entity, ExperimentalFactor factor)	Obtain the FactorValue used by the samples from this subset in the given factor.
Collection<FactorValue>	ExpressionExperimentSubSetDaoImpl.getFactorValuesUsed(ExpressionExperimentSubSet entity, ExperimentalFactor factor)
Collection<FactorValue>	ExpressionExperimentSubSetService.getFactorValuesUsed(ExpressionExperimentSubSet entity, ExperimentalFactor factor)
Collection<FactorValue>	ExpressionExperimentSubSetServiceImpl.getFactorValuesUsed(ExpressionExperimentSubSet entity, ExperimentalFactor factor)
void	ExpressionExperimentSubSetDaoImpl.remove(ExpressionExperimentSubSet entity)
void	ExpressionExperimentSubSetService.remove(ExpressionExperimentSubSet entity)	Deletes an experiment subset and all of its associated DifferentialExpressionAnalysis objects.
void	ExpressionExperimentSubSetServiceImpl.remove(ExpressionExperimentSubSet subset)	doesn't include removal of sample coexpression matrices, PCA, probe2probe coexpression links, or adjusting experiment set members

Method parameters in ubic.gemma.persistence.service.expression.experiment with type arguments of type ExpressionExperimentSubSet

Modifier and Type	Method	Description
void	ExpressionExperimentSubSetServiceImpl.remove(Collection<ExpressionExperimentSubSet> entities)

Uses of ExpressionExperimentSubSet in ubic.gemma.persistence.util

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

Modifier and Type	Method	Description
static void	BusinessKey.checkKey(ExpressionExperimentSubSet entity)
static void	BusinessKey.createQueryObject(Criteria queryObject, ExpressionExperimentSubSet entity)

Uses of ExpressionExperimentSubSet in ubic.gemma.rest

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

Constructor	Description
ExpressionExperimentSubsetWithFactorValuesObject(ExpressionExperimentSubSet subset, Set<FactorValue> factorValues, Map<ArrayDesign,ArrayDesignValueObject> id2advo, boolean includeAssays, Map<BioAssay,BioAssay> assay2sourceAssayMap)
ExpressionExperimentSubSetWithGroupsValueObject(ExpressionExperimentSubSet subset, List<Long> subSetGroupIds)

Constructor parameters in ubic.gemma.rest with type arguments of type ExpressionExperimentSubSet

Constructor	Description
BatchInformationValueObject(BatchEffectType batchEffectType, BatchEffectDetails batchEffectDetails, List<BatchConfound> batchConfound, Map<ExpressionExperimentSubSet,List<BatchConfound>> subsetBatchConfounds)

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

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

Modifier and Type	Method	Description
ExpressionExperimentSubSet	DatasetArgService.getSubSet(DatasetArg<?> datasetArg, Long subSetId)

Methods in ubic.gemma.rest.util.args that return types with arguments of type ExpressionExperimentSubSet

Modifier and Type	Method	Description
List<ExpressionExperimentSubSet>	DatasetArgService.getSubSets(DatasetArg<?> datasetArg)
Map<ExpressionExperimentSubSet,List<Long>>	DatasetArgService.getSubSetsGroupIds(DatasetArg<?> datasetArg)

Methods in ubic.gemma.rest.util.args with parameters of type ExpressionExperimentSubSet

Modifier and Type	Method	Description
List<Long>	DatasetArgService.getSubSetGroupIds(DatasetArg<?> datasetArg, ExpressionExperimentSubSet subset)