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

Packages that use RawExpressionDataVector

Package	Description
ubic.gemma.apps	This package contains built-in Gemma CLI applications.
ubic.gemma.core.analysis.preprocess	This package contains classes for preprocessing expression data.
ubic.gemma.core.analysis.singleCell.aggregate	This package contains classes for subsetting and aggregating single-cell data.
ubic.gemma.model.expression.bioAssayData
ubic.gemma.model.expression.experiment
ubic.gemma.persistence.service.expression.bioAssayData
ubic.gemma.persistence.service.expression.experiment

Uses of RawExpressionDataVector in ubic.gemma.apps

Subclasses with type arguments of type RawExpressionDataVector in ubic.gemma.apps

Modifier and Type	Class	Description
class	RawDataDeleterCli
class	RawExpressionDataWriterCli

Uses of RawExpressionDataVector in ubic.gemma.core.analysis.preprocess

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

Modifier and Type	Method	Description
Collection<RawExpressionDataVector>	TwoChannelMissingValues.computeMissingValues(ExpressionExperiment ee)
Collection<RawExpressionDataVector>	TwoChannelMissingValues.computeMissingValues(ExpressionExperiment ee, double signalToNoiseThreshold, Collection<Double> extraMissingValueIndicators)
Collection<RawExpressionDataVector>	TwoChannelMissingValuesImpl.computeMissingValues(ExpressionExperiment ee)
Collection<RawExpressionDataVector>	TwoChannelMissingValuesImpl.computeMissingValues(ExpressionExperiment ee, double signalToNoiseThreshold, Collection<Double> extraMissingValueIndicators)
Collection<RawExpressionDataVector>	TwoChannelMissingValueHelperService.persist(ExpressionExperiment source, Collection<RawExpressionDataVector> results)

Method parameters in ubic.gemma.core.analysis.preprocess with type arguments of type RawExpressionDataVector

Modifier and Type	Method	Description
Collection<RawExpressionDataVector>	TwoChannelMissingValueHelperService.persist(ExpressionExperiment source, Collection<RawExpressionDataVector> results)

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

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

Modifier and Type	Method	Description
static Collection<RawExpressionDataVector>	SingleCellDataVectorAggregatorUtils.aggregate(Collection<SingleCellExpressionDataVector> vectors, SingleCellDataVectorAggregatorUtils.SingleCellAggregationMethod method, CellLevelCharacteristics cellLevelCharacteristics, boolean aggregateUnknownCharacteristics)	Aggregate a collection of vectors.
static Function<SingleCellExpressionDataVector, RawExpressionDataVector>	SingleCellDataVectorAggregatorUtils.createAggregator(SingleCellDataVectorAggregatorUtils.SingleCellAggregationMethod method, CellLevelCharacteristics cellLevelCharacteristics, boolean aggregateUnknownCharacteristics)	Create an aggregator that can be used on a Stream of vectors.

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

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

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

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

Methods in ubic.gemma.model.expression.experiment that return types with arguments of type RawExpressionDataVector

Modifier and Type	Method	Description
Set<RawExpressionDataVector>	ExpressionExperiment.getRawExpressionDataVectors()

Method parameters in ubic.gemma.model.expression.experiment with type arguments of type RawExpressionDataVector

Modifier and Type	Method	Description
void	ExpressionExperiment.setRawExpressionDataVectors(Set<RawExpressionDataVector> rawExpressionDataVectors)

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

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

Modifier and Type	Class	Description
class	RawExpressionDataVectorDaoImpl
class	RawExpressionDataVectorServiceImpl	Provides methods that can be applied to both RawExpressionDataVector and ProcessedExpressionDataVector

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

Modifier and Type	Interface	Description
interface	RawExpressionDataVectorDao
interface	RawExpressionDataVectorService

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

Modifier and Type	Method	Description
RawExpressionDataVector	RawExpressionDataVectorDaoImpl.find(RawExpressionDataVector designElementDataVector)
RawExpressionDataVector	RawExpressionDataVectorService.load(Long id)

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

Modifier and Type	Method	Description
Collection<RawExpressionDataVector>	RawExpressionDataVectorDao.find(Collection<CompositeSequence> designElements, QuantitationType quantitationType)
Collection<RawExpressionDataVector>	RawExpressionDataVectorDao.find(ArrayDesign arrayDesign, QuantitationType quantitationType)
Collection<RawExpressionDataVector>	RawExpressionDataVectorDaoImpl.find(Collection<CompositeSequence> designElements, QuantitationType quantitationType)
Collection<RawExpressionDataVector>	RawExpressionDataVectorDaoImpl.find(ArrayDesign arrayDesign, QuantitationType quantitationType)
Collection<RawExpressionDataVector>	RawExpressionDataVectorService.find(Collection<CompositeSequence> designElements, QuantitationType quantitationType)
Collection<RawExpressionDataVector>	RawExpressionDataVectorServiceImpl.find(Collection<CompositeSequence> designElements, QuantitationType quantitationType)
Collection<RawExpressionDataVector>	RawExpressionDataVectorDao.getRandomRawVectors(QuantitationType quantitationType, int limit)	Fetch up to limit raw vectors for the given quantitation type, chosen uniformly at random.
Collection<RawExpressionDataVector>	RawExpressionDataVectorDaoImpl.getRandomRawVectors(QuantitationType quantitationType, int limit)
Collection<RawExpressionDataVector>	RawExpressionDataVectorService.getRandomRawVectors(QuantitationType quantitationType, int limit)	Fetch up to limit raw vectors for the given quantitation type, chosen uniformly at random.
Collection<RawExpressionDataVector>	RawExpressionDataVectorServiceImpl.getRandomRawVectors(QuantitationType quantitationType, int limit)

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

Modifier and Type	Method	Description
RawExpressionDataVector	RawExpressionDataVectorDaoImpl.find(RawExpressionDataVector designElementDataVector)

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

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

Modifier and Type	Method	Description
Map<QuantitationType, Collection<RawExpressionDataVector>>	ExpressionExperimentDao.getMissingValuesVectors(ExpressionExperiment ee)	Obtain the missing value vectors for a given experiment.
Map<QuantitationType, Collection<RawExpressionDataVector>>	ExpressionExperimentDaoImpl.getMissingValuesVectors(ExpressionExperiment ee)
Map<QuantitationType, Collection<RawExpressionDataVector>>	ExpressionExperimentDataVectorService.getMissingValuesVectors(ExpressionExperiment ee)
Map<QuantitationType, Collection<RawExpressionDataVector>>	ExpressionExperimentDataVectorServiceImpl.getMissingValuesVectors(ExpressionExperiment ee)
Map<QuantitationType, Collection<RawExpressionDataVector>>	ExpressionExperimentService.getMissingValuesVectors(ExpressionExperiment ee)
Map<QuantitationType, Collection<RawExpressionDataVector>>	ExpressionExperimentServiceImpl.getMissingValuesVectors(ExpressionExperiment ee)
Collection<RawExpressionDataVector>	ExpressionExperimentDao.getPreferredRawDataVectors(ExpressionExperiment ee)	Obtain the preferred raw data vectors for a given experiment.
Collection<RawExpressionDataVector>	ExpressionExperimentDaoImpl.getPreferredRawDataVectors(ExpressionExperiment ee)
Collection<RawExpressionDataVector>	ExpressionExperimentDataVectorService.getPreferredRawDataVectors(ExpressionExperiment expressionExperiment)
Collection<RawExpressionDataVector>	ExpressionExperimentDataVectorServiceImpl.getPreferredRawDataVectors(ExpressionExperiment expressionExperiment)
Collection<RawExpressionDataVector>	ExpressionExperimentService.getPreferredRawDataVectors(ExpressionExperiment expressionExperiment)
Collection<RawExpressionDataVector>	ExpressionExperimentServiceImpl.getPreferredRawDataVectors(ExpressionExperiment expressionExperiment)
Collection<RawExpressionDataVector>	ExpressionExperimentDao.getRawDataVectors(ExpressionExperiment ee, List<BioAssay> assays, QuantitationType qt)	Obtain a slice of the raw vectors for a given experiment and QT.
Collection<RawExpressionDataVector>	ExpressionExperimentDao.getRawDataVectors(ExpressionExperiment ee, QuantitationType qt)	Obtain raw vectors for a given experiment and QT.
Collection<RawExpressionDataVector>	ExpressionExperimentDaoImpl.getRawDataVectors(ExpressionExperiment ee, List<BioAssay> assays, QuantitationType qt)
Collection<RawExpressionDataVector>	ExpressionExperimentDaoImpl.getRawDataVectors(ExpressionExperiment ee, QuantitationType qt)
Collection<RawExpressionDataVector>	ExpressionExperimentDataVectorService.getRawDataVectors(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType qt)
Collection<RawExpressionDataVector>	ExpressionExperimentDataVectorService.getRawDataVectors(ExpressionExperiment ee, QuantitationType qt)
Collection<RawExpressionDataVector>	ExpressionExperimentDataVectorServiceImpl.getRawDataVectors(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType qt)
Collection<RawExpressionDataVector>	ExpressionExperimentDataVectorServiceImpl.getRawDataVectors(ExpressionExperiment ee, QuantitationType qt)
Collection<RawExpressionDataVector>	ExpressionExperimentService.getRawDataVectors(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType qt)
Collection<RawExpressionDataVector>	ExpressionExperimentService.getRawDataVectors(ExpressionExperiment ee, QuantitationType qt)
Collection<RawExpressionDataVector>	ExpressionExperimentServiceImpl.getRawDataVectors(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType qt)
Collection<RawExpressionDataVector>	ExpressionExperimentServiceImpl.getRawDataVectors(ExpressionExperiment ee, QuantitationType qt)

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

Modifier and Type	Method	Description
int	ExpressionExperimentDao.addRawDataVectors(ExpressionExperiment ee, QuantitationType qt, Collection<RawExpressionDataVector> newVectors)	Add raw data vectors with the given quantitation type.
int	ExpressionExperimentDaoImpl.addRawDataVectors(ExpressionExperiment ee, QuantitationType newQt, Collection<RawExpressionDataVector> newVectors)
int	ExpressionExperimentDataVectorService.addRawDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, Collection<RawExpressionDataVector> newVectors)	Add raw data vectors for a quantitation type.
int	ExpressionExperimentDataVectorServiceImpl.addRawDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, Collection<RawExpressionDataVector> newVectors)
int	ExpressionExperimentService.addRawDataVectors(ExpressionExperiment eeToUpdate, QuantitationType quantitationType, Collection<RawExpressionDataVector> newVectors)	Used when we want to add data for a quantitation type.
int	ExpressionExperimentServiceImpl.addRawDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, Collection<RawExpressionDataVector> newVectors)
int	ExpressionExperimentDataVectorService.replaceAllRawDataVectors(ExpressionExperiment ee, Collection<RawExpressionDataVector> vectors)	Replace all raw vectors on an experiment, grouping the input by QT and routing each group to either ExpressionExperimentDataVectorService.replaceRawDataVectors(ExpressionExperiment, QuantitationType, Collection) or ExpressionExperimentDataVectorService.addRawDataVectors(ExpressionExperiment, QuantitationType, Collection) depending on whether the QT already exists; any QT in the experiment that is no longer represented in the input is removed.
int	ExpressionExperimentDataVectorServiceImpl.replaceAllRawDataVectors(ExpressionExperiment ee, Collection<RawExpressionDataVector> newVectors)
int	ExpressionExperimentService.replaceAllRawDataVectors(ExpressionExperiment ee, Collection<RawExpressionDataVector> vectors)	Used when we are replacing data, such as when converting an experiment from one platform to another.
int	ExpressionExperimentServiceImpl.replaceAllRawDataVectors(ExpressionExperiment ee, Collection<RawExpressionDataVector> newVectors)
int	ExpressionExperimentDao.replaceRawDataVectors(ExpressionExperiment ee, QuantitationType qt, Collection<RawExpressionDataVector> vectors)	Replace raw data vectors for a given quantitation type.
int	ExpressionExperimentDaoImpl.replaceRawDataVectors(ExpressionExperiment ee, QuantitationType qt, Collection<RawExpressionDataVector> vectors)
int	ExpressionExperimentDataVectorService.replaceRawDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, Collection<RawExpressionDataVector> vectors)
int	ExpressionExperimentDataVectorServiceImpl.replaceRawDataVectors(ExpressionExperiment ee, QuantitationType qt, Collection<RawExpressionDataVector> vectors)
int	ExpressionExperimentService.replaceRawDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, Collection<RawExpressionDataVector> vectors)
int	ExpressionExperimentServiceImpl.replaceRawDataVectors(ExpressionExperiment ee, QuantitationType qt, Collection<RawExpressionDataVector> vectors)