Uses of Class
ubic.gemma.model.expression.bioAssayData.BioAssayDimension

Packages that use BioAssayDimension

Package	Description
ubic.gemma.core.analysis.expression.diff
ubic.gemma.core.analysis.singleCell.aggregate	This package contains classes for subsetting and aggregating single-cell data.
ubic.gemma.core.datastructure.matrix	This package contains data structures for representing matrices of gene expression.
ubic.gemma.core.visualization
ubic.gemma.model.analysis.expression.coexpression
ubic.gemma.model.analysis.expression.pca
ubic.gemma.model.expression.bioAssayData
ubic.gemma.persistence.service.analysis.expression.pca
ubic.gemma.persistence.service.common.quantitationtype
ubic.gemma.persistence.service.expression.bioAssay
ubic.gemma.persistence.service.expression.bioAssayData
ubic.gemma.persistence.service.expression.experiment
ubic.gemma.persistence.util
ubic.gemma.rest

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

Methods in ubic.gemma.core.analysis.expression.diff that return BioAssayDimension

Modifier and Type	Method	Description
static BioAssayDimension	DiffExAnalyzerUtils.createBADMap(List<BioMaterial> columnsToUse)

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

Methods in ubic.gemma.core.analysis.singleCell.aggregate with parameters of type BioAssayDimension

Modifier and Type	Method	Description
QuantitationType	SingleCellExpressionExperimentCreateSubSetsAndAggregateService.redoAggregate(ExpressionExperiment expressionExperiment, QuantitationType scQt, CellLevelCharacteristics clc, ExperimentalFactor factor, Map<Characteristic, FactorValue> c2f, BioAssayDimension dimension, QuantitationType previousQt, SingleCellAggregationConfig config)	Re-aggregate a dataset by any cell-level characteristics.
QuantitationType	SingleCellExpressionExperimentCreateSubSetsAndAggregateServiceImpl.redoAggregate(ExpressionExperiment expressionExperiment, QuantitationType scQt, CellLevelCharacteristics clc, ExperimentalFactor factor, Map<Characteristic, FactorValue> c2f, BioAssayDimension dimension, QuantitationType previousQt, SingleCellAggregationConfig config)
QuantitationType	SingleCellExpressionExperimentCreateSubSetsAndAggregateService.redoAggregateByCellType(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, QuantitationType previousQt, SingleCellAggregationConfig config)	Re-aggregate a dataset by cell type.
QuantitationType	SingleCellExpressionExperimentCreateSubSetsAndAggregateServiceImpl.redoAggregateByCellType(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, QuantitationType previousQt, SingleCellAggregationConfig config)

Uses of BioAssayDimension in ubic.gemma.core.datastructure.matrix

Methods in ubic.gemma.core.datastructure.matrix that return BioAssayDimension

Modifier and Type	Method	Description
BioAssayDimension	AbstractBulkExpressionDataMatrix.getBioAssayDimension()
BioAssayDimension	AbstractMultiAssayExpressionDataMatrix.getBioAssayDimension()
BioAssayDimension	AbstractMultiAssayExpressionDataMatrix.getBioAssayDimension(CompositeSequence designElement)
BioAssayDimension	BulkExpressionDataMatrix.getBioAssayDimension()	Obtain the dimension for the columns of this matrix.
BioAssayDimension	MultiAssayBulkExpressionDataMatrix.getBioAssayDimension()	Obtain the dimension for the columns of this matrix.
BioAssayDimension	MultiAssayBulkExpressionDataMatrix.getBioAssayDimension(CompositeSequence designElement)	Produce a BioAssayDimension representing the matrix columns for a specific row.

Methods in ubic.gemma.core.datastructure.matrix that return types with arguments of type BioAssayDimension

Modifier and Type	Method	Description
Optional<BioAssayDimension>	AbstractMultiAssayExpressionDataMatrix.getBestBioAssayDimension()
Optional<BioAssayDimension>	MultiAssayBulkExpressionDataMatrix.getBestBioAssayDimension()	Obtain the largest BioAssayDimension that covers all the biomaterials in this matrix.
Collection<BioAssayDimension>	AbstractMultiAssayExpressionDataMatrix.getBioAssayDimensions()
Collection<BioAssayDimension>	MultiAssayBulkExpressionDataMatrix.getBioAssayDimensions()	Obtain all the BioAssayDimensions that are used in this matrix.
List<BioAssayDimension>	TwoChannelExpressionDataMatrixBuilder.getBioAssayDimensions()	Deprecated.

Methods in ubic.gemma.core.datastructure.matrix with parameters of type BioAssayDimension

Modifier and Type	Method	Description
protected void	AbstractMultiAssayExpressionDataMatrix.addToRowMaps(CompositeSequence designElement, QuantitationType qt, BioAssayDimension dim)	Add a design element to the row maps.
BulkExpressionDataDoubleMatrix	BulkExpressionDataDoubleMatrix.sliceColumns(List<BioMaterial> bioMaterials, BioAssayDimension dimension)
BulkExpressionDataIntMatrix	BulkExpressionDataIntMatrix.sliceColumns(List<BioMaterial> bioMaterials, BioAssayDimension dimension)
BulkExpressionDataMatrix<T>	BulkExpressionDataMatrix.sliceColumns(List<BioMaterial> bioMaterials, BioAssayDimension dimension)	Slice the requested samples (columns) from this matrix.
EmptyBulkExpressionDataMatrix	EmptyBulkExpressionDataMatrix.sliceColumns(List<BioMaterial> bioMaterials, BioAssayDimension dimension)
EmptyExpressionMatrix	EmptyExpressionMatrix.sliceColumns(List<BioMaterial> bioMaterials, BioAssayDimension dimension)
ExpressionDataBooleanMatrix	ExpressionDataBooleanMatrix.sliceColumns(List<BioMaterial> bioMaterials, BioAssayDimension dimension)
ExpressionDataDoubleMatrix	ExpressionDataDoubleMatrix.sliceColumns(List<BioMaterial> bioMaterials, BioAssayDimension reorderedDim)
ExpressionDataIntegerMatrix	ExpressionDataIntegerMatrix.sliceColumns(List<BioMaterial> bioMaterials, BioAssayDimension dimension)
ExpressionDataStringMatrix	ExpressionDataStringMatrix.sliceColumns(List<BioMaterial> bioMaterials, BioAssayDimension dimension)

Constructors in ubic.gemma.core.datastructure.matrix with parameters of type BioAssayDimension

Modifier	Constructor	Description
protected	AbstractBulkExpressionDataMatrix(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, QuantitationType quantitationType, List<CompositeSequence> designElements)
	EmptyBulkExpressionDataMatrix(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, QuantitationType quantitationType)
	EmptyExpressionMatrix(ExpressionExperiment ee, BioAssayDimension ba)

Constructor parameters in ubic.gemma.core.datastructure.matrix with type arguments of type BioAssayDimension

Modifier	Constructor	Description
protected	AbstractMultiAssayExpressionDataMatrix(ExpressionExperiment ee, Collection<BioAssayDimension> dimension)
	EmptyExpressionMatrix(ExpressionExperiment ee, Collection<BioAssayDimension> dims)

Uses of BioAssayDimension in ubic.gemma.core.visualization

Methods in ubic.gemma.core.visualization that return BioAssayDimension

Modifier and Type	Method	Description
BioAssayDimension	ExpressionDataHeatmap.getDimension()
BioAssayDimension	SingleCellSparsityHeatmap.getDimension()

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

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

Constructors in ubic.gemma.core.visualization with parameters of type BioAssayDimension

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

Uses of BioAssayDimension in ubic.gemma.model.analysis.expression.coexpression

Methods in ubic.gemma.model.analysis.expression.coexpression that return BioAssayDimension

Modifier and Type	Method	Description
BioAssayDimension	SampleCoexpressionMatrix.getBioAssayDimension()

Methods in ubic.gemma.model.analysis.expression.coexpression with parameters of type BioAssayDimension

Modifier and Type	Method	Description
static SampleCoexpressionMatrix	SampleCoexpressionMatrix.Factory.newInstance(BioAssayDimension bioAssayDimension, byte[] coexpressionMatrix)
void	SampleCoexpressionMatrix.setBioAssayDimension(BioAssayDimension bioAssayDimension)

Uses of BioAssayDimension in ubic.gemma.model.analysis.expression.pca

Methods in ubic.gemma.model.analysis.expression.pca that return BioAssayDimension

Modifier and Type	Method	Description
BioAssayDimension	PrincipalComponentAnalysis.getBioAssayDimension()

Methods in ubic.gemma.model.analysis.expression.pca with parameters of type BioAssayDimension

Modifier and Type	Method	Description
void	PrincipalComponentAnalysis.setBioAssayDimension(BioAssayDimension bioAssayDimension)

Uses of BioAssayDimension in ubic.gemma.model.expression.bioAssayData

Subclasses with type arguments of type BioAssayDimension in ubic.gemma.model.expression.bioAssayData

Modifier and Type	Class	Description
class	BioAssayDimensionValueObject

Methods in ubic.gemma.model.expression.bioAssayData that return BioAssayDimension

Modifier and Type	Method	Description
BioAssayDimension	BulkExpressionDataVector.getBioAssayDimension()	A dimension of BioAssay the elements of this vector apply to.
static BioAssayDimension	BioAssayDimension.Factory.newInstance()
static BioAssayDimension	BioAssayDimension.Factory.newInstance(List<BioAssay> bioAssays)

Methods in ubic.gemma.model.expression.bioAssayData with parameters of type BioAssayDimension

Modifier and Type	Method	Description
void	BulkExpressionDataVector.setBioAssayDimension(BioAssayDimension bioAssayDimension)	A dimension of BioAssay the elements of this vector apply to.

Constructors in ubic.gemma.model.expression.bioAssayData with parameters of type BioAssayDimension

Modifier	Constructor	Description
	BioAssayDimensionValueObject(BioAssayDimension entity)

Uses of BioAssayDimension in ubic.gemma.persistence.service.analysis.expression.pca

Methods in ubic.gemma.persistence.service.analysis.expression.pca with parameters of type BioAssayDimension

Modifier and Type	Method	Description
PrincipalComponentAnalysis	PrincipalComponentAnalysisService.create(ExpressionExperiment ee, DoubleMatrix<CompositeSequence, Integer> u, double[] eigenvalues, DoubleMatrix<Integer, BioMaterial> v, BioAssayDimension bad, int numComponentsToStore, int numLoadingsToStore)
PrincipalComponentAnalysis	PrincipalComponentAnalysisServiceImpl.create(ExpressionExperiment ee, DoubleMatrix<CompositeSequence, Integer> u, double[] eigenvalues, DoubleMatrix<Integer, BioMaterial> v, BioAssayDimension bad, int numComponentsToStore, int numLoadingsToStore)
PrincipalComponentAnalysis	PrincipalComponentAnalysisService.replaceForExperiment(ExpressionExperiment ee, DoubleMatrix<CompositeSequence, Integer> u, double[] eigenvalues, DoubleMatrix<Integer, BioMaterial> v, BioAssayDimension bad, int numComponentsToStore, int numLoadingsToStore)	Remove the experiment's PCA and store the given one, in a single transaction.
PrincipalComponentAnalysis	PrincipalComponentAnalysisServiceImpl.replaceForExperiment(ExpressionExperiment ee, DoubleMatrix<CompositeSequence, Integer> u, double[] eigenvalues, DoubleMatrix<Integer, BioMaterial> v, BioAssayDimension bad, int numComponentsToStore, int numLoadingsToStore)

Uses of BioAssayDimension in ubic.gemma.persistence.service.common.quantitationtype

Methods in ubic.gemma.persistence.service.common.quantitationtype with parameters of type BioAssayDimension

Modifier and Type	Method	Description
Collection<QuantitationType>	QuantitationTypeDao.findByExpressionExperimentAndDimension(ExpressionExperiment expressionExperiment, BioAssayDimension dimension)	Retrieve all the QTs associated with the given experiment and dimension.
Collection<QuantitationType>	QuantitationTypeDao.findByExpressionExperimentAndDimension(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, Collection<Class<? extends BulkExpressionDataVector>> vectorTypes)	Retrieve all the QTs associated with the given experiment and dimension.
Collection<QuantitationType>	QuantitationTypeDaoImpl.findByExpressionExperimentAndDimension(ExpressionExperiment expressionExperiment, BioAssayDimension dimension)
Collection<QuantitationType>	QuantitationTypeDaoImpl.findByExpressionExperimentAndDimension(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, Collection<Class<? extends BulkExpressionDataVector>> vectorTypes)
Collection<QuantitationType>	QuantitationTypeReadService.findByExpressionExperimentAndDimension(ExpressionExperiment expressionExperiment, BioAssayDimension dimension)
Collection<QuantitationType>	QuantitationTypeReadService.findByExpressionExperimentAndDimension(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, Collection<Class<? extends BulkExpressionDataVector>> vectorTypes)
Collection<QuantitationType>	QuantitationTypeReadServiceImpl.findByExpressionExperimentAndDimension(ExpressionExperiment expressionExperiment, BioAssayDimension dimension)
Collection<QuantitationType>	QuantitationTypeReadServiceImpl.findByExpressionExperimentAndDimension(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, Collection<Class<? extends BulkExpressionDataVector>> vectorTypes)
Collection<QuantitationType>	QuantitationTypeService.findByExpressionExperimentAndDimension(ExpressionExperiment expressionExperiment, BioAssayDimension dimension)
Collection<QuantitationType>	QuantitationTypeService.findByExpressionExperimentAndDimension(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, Collection<Class<? extends BulkExpressionDataVector>> dataVectorTypes)
Collection<QuantitationType>	QuantitationTypeServiceImpl.findByExpressionExperimentAndDimension(ExpressionExperiment expressionExperiment, BioAssayDimension dimension)
Collection<QuantitationType>	QuantitationTypeServiceImpl.findByExpressionExperimentAndDimension(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, Collection<Class<? extends BulkExpressionDataVector>> vectorTypes)

Uses of BioAssayDimension in ubic.gemma.persistence.service.expression.bioAssay

Methods in ubic.gemma.persistence.service.expression.bioAssay that return types with arguments of type BioAssayDimension

Modifier and Type	Method	Description
Collection<BioAssayDimension>	BioAssayDao.findBioAssayDimensions(BioAssay bioAssay)
Collection<BioAssayDimension>	BioAssayDaoImpl.findBioAssayDimensions(BioAssay bioAssay)
Collection<BioAssayDimension>	BioAssayReadService.findBioAssayDimensions(BioAssay bioAssay)	Locate all BioAssayDimensions in which the selected BioAssay occurs.
Collection<BioAssayDimension>	BioAssayReadServiceImpl.findBioAssayDimensions(BioAssay bioAssay)
Collection<BioAssayDimension>	BioAssayService.findBioAssayDimensions(BioAssay bioAssay)	Locate all BioAssayDimensions in which the selected BioAssay occurs
Collection<BioAssayDimension>	BioAssayServiceImpl.findBioAssayDimensions(BioAssay bioAssay)

Uses of BioAssayDimension in ubic.gemma.persistence.service.expression.bioAssayData

Subclasses with type arguments of type BioAssayDimension in ubic.gemma.persistence.service.expression.bioAssayData

Modifier and Type	Class	Description
class	BioAssayDimensionDaoImpl	Base Spring DAO Class: is able to create, update, remove, load, and find objects of type ubic.gemma.model.expression.bioAssayData.BioAssayDimension.
class	BioAssayDimensionServiceImpl	Spring Service base class for BioAssayDimensionService, provides access to all services and entities referenced by this service.

Subinterfaces with type arguments of type BioAssayDimension in ubic.gemma.persistence.service.expression.bioAssayData

Modifier and Type	Interface	Description
interface	BioAssayDimensionDao
interface	BioAssayDimensionService
interface	BioAssayDimensionService

Methods in ubic.gemma.persistence.service.expression.bioAssayData that return BioAssayDimension

Modifier and Type	Method	Description
BioAssayDimension	BioAssayDimensionService.create(BioAssayDimension bioAssayDimension)
BioAssayDimension	BioAssayDimensionDaoImpl.find(BioAssayDimension bioAssayDimension)	Find a BioAssayDimension with the exact same list of BioAssays, name and description.
BioAssayDimension	BioAssayDimensionService.findOrCreate(BioAssayDimension bioAssayDimension)
BioAssayDimension	BioAssayDimensionService.thaw(BioAssayDimension bioAssayDimension)	Fully thaw a dimension.
BioAssayDimension	BioAssayDimensionServiceImpl.thaw(BioAssayDimension bioAssayDimension)
BioAssayDimension	BioAssayDimensionService.thawLite(BioAssayDimension bioAssayDimension)	Lightly thaw a dimension.
BioAssayDimension	BioAssayDimensionServiceImpl.thawLite(BioAssayDimension bioAssayDimension)

Methods in ubic.gemma.persistence.service.expression.bioAssayData that return types with arguments of type BioAssayDimension

Modifier and Type	Method	Description
Collection<BioAssayDimension>	BioAssayDimensionDao.findByBioAssaysContainingAll(Collection<BioAssay> bioAssays)	Find all the dimensions that contains all the given assays.
Collection<BioAssayDimension>	BioAssayDimensionDaoImpl.findByBioAssaysContainingAll(Collection<BioAssay> bioAssays)
Collection<BioAssayDimension>	BioAssayDimensionService.findByBioAssaysContainingAll(Collection<BioAssay> bioAssays)
Collection<BioAssayDimension>	BioAssayDimensionServiceImpl.findByBioAssaysContainingAll(Collection<BioAssay> bioAssays)

Methods in ubic.gemma.persistence.service.expression.bioAssayData with parameters of type BioAssayDimension

Modifier and Type	Method	Description
BioAssayDimension	BioAssayDimensionService.create(BioAssayDimension bioAssayDimension)
protected BioAssayDimensionValueObject	BioAssayDimensionDaoImpl.doLoadValueObject(BioAssayDimension entity)
Collection<T>	AbstractBulkExpressionDataVectorService.find(BioAssayDimension bioAssayDimension)
Collection<T>	AbstractDesignElementDataVectorDao.find(BioAssayDimension bioAssayDimension)
BioAssayDimension	BioAssayDimensionDaoImpl.find(BioAssayDimension bioAssayDimension)	Find a BioAssayDimension with the exact same list of BioAssays, name and description.
Collection<T>	BulkExpressionDataVectorService.find(BioAssayDimension bioAssayDimension)	Find specific type (raw or processed, depending on the service) of vectors that meet the given criteria.
Collection<T>	DesignElementDataVectorDao.find(BioAssayDimension bioAssayDimension)
Collection<T>	AbstractBulkExpressionDataVectorService.findAndThaw(BioAssayDimension bioAssayDimension)
Collection<T>	BulkExpressionDataVectorService.findAndThaw(BioAssayDimension bioAssayDimension)
Collection<BulkExpressionDataVector>	RawAndProcessedExpressionDataVectorServiceImpl.findAndThaw(BioAssayDimension bioAssayDimension)
BioAssayDimension	BioAssayDimensionService.findOrCreate(BioAssayDimension bioAssayDimension)
Slice<ProcessedExpressionDataVector>	ProcessedExpressionDataVectorService.getProcessedDataVectors(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, int offset, int limit)
Slice<ProcessedExpressionDataVector>	ProcessedExpressionDataVectorServiceImpl.getProcessedDataVectors(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, int offset, int limit)
Slice<CompositeSequence>	ProcessedExpressionDataVectorService.getProcessedDataVectorsDesignElements(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, int offset, int limit)
Slice<CompositeSequence>	ProcessedExpressionDataVectorServiceImpl.getProcessedDataVectorsDesignElements(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, int offset, int limit)
List<ProcessedExpressionDataVector>	ProcessedExpressionDataVectorDao.getProcessedVectors(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, int offset, int limit)	Retrieve a slice of processed vectors.
List<ProcessedExpressionDataVector>	ProcessedExpressionDataVectorDaoImpl.getProcessedVectors(ExpressionExperiment ee, BioAssayDimension dimension, int offset, int limit)
List<CompositeSequence>	ProcessedExpressionDataVectorDao.getProcessedVectorsDesignElements(ExpressionExperiment ee, BioAssayDimension dimension, int offset, int limit)	Only retrieve the design elements for a slice of vectors.
List<CompositeSequence>	ProcessedExpressionDataVectorDaoImpl.getProcessedVectorsDesignElements(ExpressionExperiment ee, BioAssayDimension dimension, int offset, int limit)
void	BioAssayDimensionService.remove(BioAssayDimension bioAssayDimension)
BioAssayDimension	BioAssayDimensionService.thaw(BioAssayDimension bioAssayDimension)	Fully thaw a dimension.
BioAssayDimension	BioAssayDimensionServiceImpl.thaw(BioAssayDimension bioAssayDimension)
BioAssayDimension	BioAssayDimensionService.thawLite(BioAssayDimension bioAssayDimension)	Lightly thaw a dimension.
BioAssayDimension	BioAssayDimensionServiceImpl.thawLite(BioAssayDimension bioAssayDimension)

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

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

Modifier and Type	Method	Description
BioAssayDimension	ExpressionExperimentDao.getBioAssayDimension(ExpressionExperiment ee, QuantitationType qt)	Retrieve a dimension for a given experiment and quantitation type.
BioAssayDimension	ExpressionExperimentDao.getBioAssayDimension(ExpressionExperiment ee, QuantitationType qt, Class<? extends BulkExpressionDataVector> dataVectorType)	Retrieve a dimension for a given experiment and quantitation type.
BioAssayDimension	ExpressionExperimentDaoImpl.getBioAssayDimension(ExpressionExperiment ee, QuantitationType qt)
BioAssayDimension	ExpressionExperimentDaoImpl.getBioAssayDimension(ExpressionExperiment ee, QuantitationType qt, Class<? extends BulkExpressionDataVector> dataVectorType)
BioAssayDimension	ExpressionExperimentService.getBioAssayDimension(ExpressionExperiment ee, QuantitationType qt)	Obtain the dimension associated to the given quantitation type for the given experiment.
BioAssayDimension	ExpressionExperimentService.getBioAssayDimension(ExpressionExperiment ee, QuantitationType qt, Class<? extends BulkExpressionDataVector> dataVectorType)
BioAssayDimension	ExpressionExperimentServiceImpl.getBioAssayDimension(ExpressionExperiment ee, QuantitationType qt)
BioAssayDimension	ExpressionExperimentServiceImpl.getBioAssayDimension(ExpressionExperiment ee, QuantitationType qt, Class<? extends BulkExpressionDataVector> dataVectorType)
BioAssayDimension	ExpressionExperimentDao.getBioAssayDimensionById(ExpressionExperiment ee, Long dimensionId, Class<? extends BulkExpressionDataVector> dataVectorType)	Obtain a bioassay dimension by ID.
BioAssayDimension	ExpressionExperimentDaoImpl.getBioAssayDimensionById(ExpressionExperiment ee, Long dimensionId, Class<? extends BulkExpressionDataVector> dataVectorType)
BioAssayDimension	ExpressionExperimentService.getBioAssayDimensionById(ExpressionExperiment ee, Long dimensionId)	Find a BioAssayDimension by ID.
BioAssayDimension	ExpressionExperimentService.getBioAssayDimensionById(ExpressionExperiment ee, Long dimensionId, Class<? extends BulkExpressionDataVector> dataVectorType)
BioAssayDimension	ExpressionExperimentServiceImpl.getBioAssayDimensionById(ExpressionExperiment ee, Long dimensionId)
BioAssayDimension	ExpressionExperimentServiceImpl.getBioAssayDimensionById(ExpressionExperiment ee, Long dimensionId, Class<? extends BulkExpressionDataVector> dataVectorType)
BioAssayDimension	ExpressionExperimentDao.getProcessedBioAssayDimension(ExpressionExperiment ee)	Retrieve the dimension associated to the procesed data vectors.
BioAssayDimension	ExpressionExperimentDaoImpl.getProcessedBioAssayDimension(ExpressionExperiment ee)
BioAssayDimension	ExpressionExperimentService.getProcessedBioAssayDimension(ExpressionExperiment ee)	Obtain the dimension associated to the processed data for the given experiment.
BioAssayDimension	ExpressionExperimentServiceImpl.getProcessedBioAssayDimension(ExpressionExperiment ee)

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

Modifier and Type	Method	Description
Collection<BioAssayDimension>	ExpressionExperimentDao.getBioAssayDimensions(ExpressionExperiment expressionExperiment)
Collection<BioAssayDimension>	ExpressionExperimentDao.getBioAssayDimensions(ExpressionExperiment ee, QuantitationType qt)
Collection<BioAssayDimension>	ExpressionExperimentDao.getBioAssayDimensions(ExpressionExperiment ee, QuantitationType qt, Class<? extends BulkExpressionDataVector> dataVectorType)
Collection<BioAssayDimension>	ExpressionExperimentDaoImpl.getBioAssayDimensions(ExpressionExperiment expressionExperiment)
Collection<BioAssayDimension>	ExpressionExperimentDaoImpl.getBioAssayDimensions(ExpressionExperiment ee, QuantitationType qt)
Collection<BioAssayDimension>	ExpressionExperimentDaoImpl.getBioAssayDimensions(ExpressionExperiment ee, QuantitationType qt, Class<? extends BulkExpressionDataVector> dataVectorType)
Collection<BioAssayDimension>	ExpressionExperimentService.getBioAssayDimensionsWithAssays(ExpressionExperiment expressionExperiment)	Obtain all the dimensions associated to the given experiment.
Collection<BioAssayDimension>	ExpressionExperimentService.getBioAssayDimensionsWithAssays(ExpressionExperiment ee, QuantitationType qt)	Obtain all BioAssayDimensions associated to a particular QuantitationType.
Collection<BioAssayDimension>	ExpressionExperimentServiceImpl.getBioAssayDimensionsWithAssays(ExpressionExperiment expressionExperiment)
Collection<BioAssayDimension>	ExpressionExperimentServiceImpl.getBioAssayDimensionsWithAssays(ExpressionExperiment ee, QuantitationType qt)
Map<ExpressionExperiment, Collection<BioAssayDimension>>	ExpressionExperimentDao.getProcessedBioAssayDimensions(Collection<ExpressionExperiment> ees)	Batched variant of ExpressionExperimentDao.getProcessedBioAssayDimensions(ExpressionExperiment) — one HQL with an IN clause for the supplied experiments.
Collection<BioAssayDimension>	ExpressionExperimentDao.getProcessedBioAssayDimensions(ExpressionExperiment ee)
Map<ExpressionExperiment, Collection<BioAssayDimension>>	ExpressionExperimentDaoImpl.getProcessedBioAssayDimensions(Collection<ExpressionExperiment> ees)
Collection<BioAssayDimension>	ExpressionExperimentDaoImpl.getProcessedBioAssayDimensions(ExpressionExperiment ee)
Collection<BioAssayDimension>	ExpressionExperimentService.getProcessedBioAssayDimensionsWithAssays(ExpressionExperiment ee)	Obtain the dimension associated to the processed data for the given experiment.
Collection<BioAssayDimension>	ExpressionExperimentServiceImpl.getProcessedBioAssayDimensionsWithAssays(ExpressionExperiment ee)
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)

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

Modifier and Type	Method	Description
Collection<QuantitationType>	ExpressionExperimentService.getQuantitationTypes(ExpressionExperiment expressionExperiment, BioAssayDimension dimension)	Retrieve all the quantitation types used by the given experiment and dimension.
Collection<QuantitationType>	ExpressionExperimentService.getQuantitationTypes(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, Class<? extends BulkExpressionDataVector> dataVectorType)
Collection<QuantitationType>	ExpressionExperimentServiceImpl.getQuantitationTypes(ExpressionExperiment expressionExperiment, BioAssayDimension dimension)
Collection<QuantitationType>	ExpressionExperimentServiceImpl.getQuantitationTypes(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, Class<? extends BulkExpressionDataVector> dataVectorType)
Collection<ExpressionExperimentSubSet>	ExpressionExperimentDao.getSubSets(ExpressionExperiment expressionExperiment, BioAssayDimension bad)
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<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)
Collection<ExpressionExperimentSubSet>	ExpressionExperimentService.getSubSetsWithBioAssays(ExpressionExperiment expressionExperiment, BioAssayDimension dimension)	Obtain the subsets for a particular dimension.
Collection<ExpressionExperimentSubSet>	ExpressionExperimentServiceImpl.getSubSetsWithBioAssays(ExpressionExperiment expressionExperiment, BioAssayDimension dimension)
Collection<ExpressionExperimentSubSet>	ExpressionExperimentSubSetReadService.getSubSetsWithBioAssays(ExpressionExperiment expressionExperiment, BioAssayDimension dimension)	Obtain the subsets for a particular dimension, with assays lightly thawed.
Collection<ExpressionExperimentSubSet>	ExpressionExperimentSubSetReadServiceImpl.getSubSetsWithBioAssays(ExpressionExperiment expressionExperiment, BioAssayDimension dimension)

Uses of BioAssayDimension in ubic.gemma.persistence.util

Methods in ubic.gemma.persistence.util that return BioAssayDimension

Modifier and Type	Method	Description
static BioAssayDimension	BusinessKey.find(Session session, BioAssayDimension bioAssayDimension)

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

Modifier and Type	Method	Description
static void	BusinessKey.checkKey(BioAssayDimension bioAssayDimension)
static BioAssayDimension	BusinessKey.find(Session session, BioAssayDimension bioAssayDimension)
static void	Thaws.thawBioAssayDimension(BioAssayDimension bioAssayDimension)

Uses of BioAssayDimension in ubic.gemma.rest

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

Modifier	Constructor	Description
	ExpressionExperimentSubSetGroupValueObject(BioAssayDimension bioAssayDimension, List<DatasetsWebService.ExpressionExperimentSubsetWithFactorValuesObject> subSets, List<ExperimentalFactorValueObject> factors, List<QuantitationTypeValueObject> quantitationTypes)