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

Packages that use ExpressionExperimentSubSet

Package	Description
ubic.gemma.core.analysis.expression.diff
ubic.gemma.core.analysis.preprocess.batcheffects
ubic.gemma.core.analysis.singleCell	This package contains classes for analysing single-cell expression data.
ubic.gemma.core.analysis.singleCell.aggregate	This package contains classes for subsetting and aggregating single-cell data.
ubic.gemma.core.visualization
ubic.gemma.model.expression.experiment
ubic.gemma.persistence.service.expression.bioAssay
ubic.gemma.persistence.service.expression.experiment
ubic.gemma.persistence.util
ubic.gemma.rest
ubic.gemma.rest.util.args

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)	Check if a factor value should be excluded from the analysis.

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

Method parameters in ubic.gemma.core.analysis.singleCell 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.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>	SingleCellExpressionExperimentSubSetService.createSubSets(ExpressionExperiment ee, SingleCellDimension scd, CellLevelCharacteristics clc, ExperimentalFactor factor, Map<Characteristic, FactorValue> cellTypeMapping, SingleCellExperimentSubSetsCreationConfig config)	Subset biomaterials and bioassays by the given CellLevelCharacteristics.
List<ExpressionExperimentSubSet>	SingleCellExpressionExperimentSubSetServiceImpl.createSubSets(ExpressionExperiment ee, SingleCellDimension scd, CellLevelCharacteristics clc, ExperimentalFactor factor, Map<Characteristic, FactorValue> mappedCellTypeFactors, SingleCellExperimentSubSetsCreationConfig config)
List<ExpressionExperimentSubSet>	SingleCellExpressionExperimentSubSetService.createSubSetsByCellType(ExpressionExperiment ee, SingleCellExperimentSubSetsCreationConfig config)	Subset a single-cell dataset by preferred cell type assignment the cell type factor and the
List<ExpressionExperimentSubSet>	SingleCellExpressionExperimentSubSetServiceImpl.createSubSetsByCellType(ExpressionExperiment ee, SingleCellExperimentSubSetsCreationConfig config)

Uses of ExpressionExperimentSubSet in ubic.gemma.core.visualization

Methods in ubic.gemma.core.visualization that return types with arguments of type ExpressionExperimentSubSet

Modifier and Type	Method	Description
List<ExpressionExperimentSubSet>	SingleCellSparsityHeatmap.getSubSets()

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

Modifier	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

Subclasses with type arguments of type ExpressionExperimentSubSet in ubic.gemma.model.expression.experiment

Modifier and Type	Class	Description
class	ExpressionExperimentSubsetValueObject

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

Modifier and Type	Method	Description
static ExpressionExperimentSubSet	ExpressionExperimentSubSet.Factory.newInstance(String name, ExpressionExperiment sourceExperiment)	Subsets are named by appending the name to the source experiment name, separated by ExpressionExperimentSubSet.NAME_DELIMITER.

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

Modifier and Type	Method	Description
static String	ExpressionExperimentSubSetUtils.getUnprefixedName(ExpressionExperimentSubSet subset)	Obtain the unprefixed name of a subset, i.e., the name without the source experiment name and delimiter.

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

Modifier	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.bioAssay

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

Modifier and Type	Method	Description
CursorPage<BioAssayValueObject>	BioAssayDao.loadValueObjectsByCursorForSubSet(ExpressionExperimentSubSet subset, Cursor cursor, int limit)	Cursor-paged listing of BioAssayValueObjects for a single ExpressionExperimentSubSet, sorted by ascending id — see CURSOR_PAGINATION_STEP1_PLAN.md step 1u (the subset-scoped twin of step 1k).
CursorPage<BioAssayValueObject>	BioAssayDaoImpl.loadValueObjectsByCursorForSubSet(ExpressionExperimentSubSet subset, Cursor cursor, int limit)
CursorPage<BioAssayValueObject>	BioAssayReadService.loadValueObjectsByCursorForSubSet(ExpressionExperimentSubSet subset, Cursor cursor, int limit)
CursorPage<BioAssayValueObject>	BioAssayReadServiceImpl.loadValueObjectsByCursorForSubSet(ExpressionExperimentSubSet subset, Cursor cursor, int limit)
CursorPage<BioAssayValueObject>	BioAssayService.loadValueObjectsByCursorForSubSet(ExpressionExperimentSubSet subset, Cursor cursor, int limit)	Cursor-mode counterpart to the legacy unpaginated subset-scoped sample listing — see CURSOR_PAGINATION_STEP1_PLAN.md step 1u.
CursorPage<BioAssayValueObject>	BioAssayServiceImpl.loadValueObjectsByCursorForSubSet(ExpressionExperimentSubSet subset, Cursor cursor, int limit)

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

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

Modifier and Type	Class	Description
class	ExpressionExperimentSubSetDaoImpl	Base Spring DAO Class: is able to create, update, remove, load, and find objects of type ubic.gemma.model.expression.experiment.ExpressionExperimentSubSet.
class	ExpressionExperimentSubSetServiceImpl

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

Modifier and Type	Interface	Description
interface	ExpressionExperimentSubSetDao
interface	ExpressionExperimentSubSetService

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	ExpressionExperimentSubSetReadService.getSubSetByIdWithCharacteristics(ExpressionExperiment ee, Long subSetId)	Obtain a particular subset by ID, with characteristics initialized.
ExpressionExperimentSubSet	ExpressionExperimentSubSetReadServiceImpl.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	ExpressionExperimentSubSetReadService.getSubSetByIdWithCharacteristicsAndBioAssays(ExpressionExperiment ee, Long subSetId)	Obtain a particular subset by ID, with characteristics initialized and assays thawed.
ExpressionExperimentSubSet	ExpressionExperimentSubSetReadServiceImpl.getSubSetByIdWithCharacteristicsAndBioAssays(ExpressionExperiment ee, Long subSetId)
ExpressionExperimentSubSet	ExpressionExperimentSubSetService.load(Long id)
ExpressionExperimentSubSet	ExpressionExperimentSubSetReadService.loadSubSet(Long id)	Load a subset by ID, without initializing collections.
ExpressionExperimentSubSet	ExpressionExperimentSubSetReadServiceImpl.loadSubSet(Long id)
ExpressionExperimentSubSet	ExpressionExperimentSubSetReadService.loadSubSetWithBioAssays(Long id)	Load a subset by ID with its bio-assays initialized.
ExpressionExperimentSubSet	ExpressionExperimentSubSetReadServiceImpl.loadSubSetWithBioAssays(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>	ExpressionExperimentSubSetReadService.findByBioAssayIn(Collection<BioAssay> bioAssays)	Find every subset that contains any of the supplied bio-assays.
Collection<ExpressionExperimentSubSet>	ExpressionExperimentSubSetReadServiceImpl.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)
Collection<ExpressionExperimentSubSet>	ExpressionExperimentSubSetReadService.getSubSets(ExpressionExperiment expressionExperiment, BioAssayDimension dimension)	Obtain the subsets for a particular dimension.
Collection<ExpressionExperimentSubSet>	ExpressionExperimentSubSetReadServiceImpl.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>>	ExpressionExperimentSubSetReadService.getSubSetsByDimension(ExpressionExperiment expressionExperiment)	Obtain all the subsets organized by dimension for a given dataset.
Map<BioAssayDimension, Set<ExpressionExperimentSubSet>>	ExpressionExperimentSubSetReadServiceImpl.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<BioAssayDimension, Set<ExpressionExperimentSubSet>>	ExpressionExperimentSubSetReadService.getSubSetsByDimensionWithBioAssays(ExpressionExperiment expressionExperiment)	Obtain all the subsets organized by dimension for a given dataset, with assays thawed.
Map<BioAssayDimension, Set<ExpressionExperimentSubSet>>	ExpressionExperimentSubSetReadServiceImpl.getSubSetsByDimensionWithBioAssays(ExpressionExperiment expressionExperiment)
Map<ExpressionExperiment, Collection<ExpressionExperimentSubSet>>	ExpressionExperimentDao.getSubSetsByExpressionExperiments(Collection<ExpressionExperiment> expressionExperiments)	Batched variant of ExpressionExperimentDao.getSubSets(ExpressionExperiment): obtain subsets for every experiment in the input collection in a single query, keyed by source experiment.
Map<ExpressionExperiment, Collection<ExpressionExperimentSubSet>>	ExpressionExperimentDaoImpl.getSubSetsByExpressionExperiments(Collection<ExpressionExperiment> expressionExperiments)
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<ExperimentalFactor, Map<FactorValue, ExpressionExperimentSubSet>>	ExpressionExperimentSubSetReadService.getSubSetsByFactorValue(ExpressionExperiment expressionExperiment, BioAssayDimension dimension)	Reconstitute the FV-to-subset mapping for a given experiment along all separating factors.
Map<FactorValue, ExpressionExperimentSubSet>	ExpressionExperimentSubSetReadService.getSubSetsByFactorValue(ExpressionExperiment expressionExperiment, ExperimentalFactor experimentalFactor, BioAssayDimension dimension)	Reconstitute the FV-to-subset mapping for a given experiment and factor.
Map<ExperimentalFactor, Map<FactorValue, ExpressionExperimentSubSet>>	ExpressionExperimentSubSetReadServiceImpl.getSubSetsByFactorValue(ExpressionExperiment expressionExperiment, BioAssayDimension dimension)
Map<FactorValue, ExpressionExperimentSubSet>	ExpressionExperimentSubSetReadServiceImpl.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)
Map<FactorValue, ExpressionExperimentSubSet>	ExpressionExperimentSubSetReadService.getSubSetsByFactorValueWithCharacteristicsAndBioAssays(ExpressionExperiment expressionExperiment, ExperimentalFactor experimentalFactor, BioAssayDimension dimension)	Reconstitute the FV-to-subset mapping for a given experiment and factor, with subset characteristics initialized and assays thawed.
Map<FactorValue, ExpressionExperimentSubSet>	ExpressionExperimentSubSetReadServiceImpl.getSubSetsByFactorValueWithCharacteristicsAndBioAssays(ExpressionExperiment expressionExperiment, ExperimentalFactor experimentalFactor, BioAssayDimension dimension)
Map<ExpressionExperiment, Collection<ExpressionExperimentSubSet>>	ExpressionExperimentService.getSubSetsWithBioAssays(Collection<ExpressionExperiment> expressionExperiments)	Batched variant of ExpressionExperimentService.getSubSetsWithBioAssays(ExpressionExperiment): obtain subsets for every experiment in the input collection in a single query, keyed by source experiment.
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.
Map<ExpressionExperiment, Collection<ExpressionExperimentSubSet>>	ExpressionExperimentServiceImpl.getSubSetsWithBioAssays(Collection<ExpressionExperiment> expressionExperiments)
Collection<ExpressionExperimentSubSet>	ExpressionExperimentServiceImpl.getSubSetsWithBioAssays(ExpressionExperiment expressionExperiment)
Collection<ExpressionExperimentSubSet>	ExpressionExperimentServiceImpl.getSubSetsWithBioAssays(ExpressionExperiment expressionExperiment, BioAssayDimension dimension)
Map<ExpressionExperiment, Collection<ExpressionExperimentSubSet>>	ExpressionExperimentSubSetReadService.getSubSetsWithBioAssays(Collection<ExpressionExperiment> expressionExperiments)	Batched variant: obtain subsets for every experiment in the input collection in a single query, keyed by source experiment.
Collection<ExpressionExperimentSubSet>	ExpressionExperimentSubSetReadService.getSubSetsWithBioAssays(ExpressionExperiment expressionExperiment)	Obtain all the subsets for a given dataset.
Collection<ExpressionExperimentSubSet>	ExpressionExperimentSubSetReadService.getSubSetsWithBioAssays(ExpressionExperiment expressionExperiment, BioAssayDimension dimension)	Obtain the subsets for a particular dimension, with assays lightly thawed.
Map<ExpressionExperiment, Collection<ExpressionExperimentSubSet>>	ExpressionExperimentSubSetReadServiceImpl.getSubSetsWithBioAssays(Collection<ExpressionExperiment> expressionExperiments)
Collection<ExpressionExperimentSubSet>	ExpressionExperimentSubSetReadServiceImpl.getSubSetsWithBioAssays(ExpressionExperiment expressionExperiment)
Collection<ExpressionExperimentSubSet>	ExpressionExperimentSubSetReadServiceImpl.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>	ExpressionExperimentSubSetReadService.getSubSetsWithCharacteristics(ExpressionExperiment ee)	Obtain all the subsets for a given dataset, with characteristics initialized.
Collection<ExpressionExperimentSubSet>	ExpressionExperimentSubSetReadServiceImpl.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>	ExpressionExperimentReadService.getAnnotations(ExpressionExperimentSubSet ee)
Set<AnnotationValueObject>	ExpressionExperimentReadService.getAnnotations(ExpressionExperimentSubSet ee, boolean includeFreeText)
Set<AnnotationValueObject>	ExpressionExperimentReadServiceImpl.getAnnotations(ExpressionExperimentSubSet ee)
Set<AnnotationValueObject>	ExpressionExperimentReadServiceImpl.getAnnotations(ExpressionExperimentSubSet ee, boolean includeFreeText)
Set<AnnotationValueObject>	ExpressionExperimentService.getAnnotations(ExpressionExperimentSubSet ee)	Retrieve annotations for a given experiment subset.
Set<AnnotationValueObject>	ExpressionExperimentService.getAnnotations(ExpressionExperimentSubSet ee, boolean includeFreeText)	Retrieve annotations for a given experiment subset, optionally including unmapped ones.
Set<AnnotationValueObject>	ExpressionExperimentServiceImpl.getAnnotations(ExpressionExperimentSubSet ee)
Set<AnnotationValueObject>	ExpressionExperimentServiceImpl.getAnnotations(ExpressionExperimentSubSet ee, boolean includeFreeText)
Collection<ArrayDesign>	ExpressionExperimentSubSetDao.getArrayDesignsUsed(ExpressionExperimentSubSet subset)
Collection<ArrayDesign>	ExpressionExperimentSubSetDaoImpl.getArrayDesignsUsed(ExpressionExperimentSubSet subset)
Collection<ArrayDesign>	ExpressionExperimentSubSetReadService.getArrayDesignsUsed(ExpressionExperimentSubSet subset)	Obtain the array designs used by the assays in the subset.
Collection<ArrayDesign>	ExpressionExperimentSubSetReadServiceImpl.getArrayDesignsUsed(ExpressionExperimentSubSet subset)
Collection<ArrayDesign>	ExpressionExperimentSubSetService.getArrayDesignsUsed(ExpressionExperimentSubSet subset)
Collection<ArrayDesign>	ExpressionExperimentSubSetServiceImpl.getArrayDesignsUsed(ExpressionExperimentSubSet subset)
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)
List<Object[]>	ExpressionExperimentDao.getFactorValueAnnotationsWithParents(ExpressionExperimentSubSet subset)	Subset variant of ExpressionExperimentDao.getFactorValueAnnotationsWithParents(ExpressionExperiment).
List<Object[]>	ExpressionExperimentDaoImpl.getFactorValueAnnotationsWithParents(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>	ExpressionExperimentSubSetReadService.getFactorValuesUsed(ExpressionExperimentSubSet entity, ExperimentalFactor factor)	Obtain the FactorValues used by samples in the given subset for the given factor.
Collection<FactorValue>	ExpressionExperimentSubSetReadServiceImpl.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 that return ExpressionExperimentSubSet

Modifier and Type	Method	Description
static ExpressionExperimentSubSet	BusinessKey.find(Session session, ExpressionExperimentSubSet entity)

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

Modifier and Type	Method	Description
static void	BusinessKey.checkKey(ExpressionExperimentSubSet entity)
static ExpressionExperimentSubSet	BusinessKey.find(Session session, ExpressionExperimentSubSet entity)

Uses of ExpressionExperimentSubSet in ubic.gemma.rest

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

Modifier	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

Modifier	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)