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

Packages that use ProcessedExpressionDataVector

Package	Description
ubic.gemma.apps	This package contains built-in Gemma CLI applications.
ubic.gemma.core.analysis.service
ubic.gemma.core.datastructure.matrix	This package contains data structures for representing matrices of gene expression.
ubic.gemma.model.expression.bioAssayData
ubic.gemma.model.expression.experiment
ubic.gemma.persistence.service.expression.bioAssayData
ubic.gemma.persistence.service.expression.experiment

Uses of ProcessedExpressionDataVector in ubic.gemma.apps

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

Modifier and Type	Class	Description
class	ProcessedDataDeleterCli

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

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

Modifier and Type	Method	Description
ExpressionDataDoubleMatrix	ExpressionDataMatrixService.getFilteredMatrix(Collection<ProcessedExpressionDataVector> dataVectors, ArrayDesign arrayDesign, ExpressionExperimentFilterConfig filterConfig, boolean logTransform)
ExpressionDataDoubleMatrix	ExpressionDataMatrixService.getFilteredMatrix(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> dataVectors, ExpressionExperimentFilterConfig filterConfig, boolean logTransform)	Provide a filtered expression data matrix.
ExpressionDataDoubleMatrix	ExpressionDataMatrixService.getFilteredMatrix(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> dataVectors, ExpressionExperimentFilterConfig filterConfig, boolean logTransform, ExpressionExperimentFilterResult result)	Provide a filtered expression data matrix, reporting the per-stage attrition into a caller-supplied result.
ExpressionDataDoubleMatrix	ExpressionDataMatrixServiceImpl.getFilteredMatrix(Collection<ProcessedExpressionDataVector> dataVectors, ArrayDesign arrayDesign, ExpressionExperimentFilterConfig filterConfig, boolean logTransform)
ExpressionDataDoubleMatrix	ExpressionDataMatrixServiceImpl.getFilteredMatrix(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> dataVectors, ExpressionExperimentFilterConfig filterConfig, boolean logTransform)
ExpressionDataDoubleMatrix	ExpressionDataMatrixServiceImpl.getFilteredMatrix(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> dataVectors, ExpressionExperimentFilterConfig filterConfig, boolean logTransform, ExpressionExperimentFilterResult result)

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

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

Modifier	Constructor	Description
	TwoChannelExpressionDataMatrixBuilder(Collection<ProcessedExpressionDataVector> processedVectors, Collection<? extends BulkExpressionDataVector> otherVectors)	Deprecated.

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

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

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

Methods in ubic.gemma.model.expression.bioAssayData that return types with arguments of type ProcessedExpressionDataVector

Modifier and Type	Method	Description
static Collection<ProcessedExpressionDataVector>	DoubleVectorValueObjectUtils.toBulkVectors(Collection<DoubleVectorValueObject> vectors)	Convert a collection of DoubleVectorValueObject.

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

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

Modifier and Type	Method	Description
Set<ProcessedExpressionDataVector>	ExpressionExperiment.getProcessedExpressionDataVectors()

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

Modifier and Type	Method	Description
void	ExpressionExperiment.setProcessedExpressionDataVectors(Set<ProcessedExpressionDataVector> processedExpressionDataVectors)

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

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

Modifier and Type	Class	Description
class	ProcessedExpressionDataVectorDaoImpl
class	ProcessedExpressionDataVectorServiceImpl

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

Modifier and Type	Interface	Description
interface	ProcessedExpressionDataVectorDao
interface	ProcessedExpressionDataVectorService

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

Modifier and Type	Method	Description
Collection<ProcessedExpressionDataVector>	ProcessedExpressionDataVectorDao.find(Collection<CompositeSequence> designElements, QuantitationType quantitationType)	Retrieve the processed vectors for a set of design elements within a given quantitation type.
Collection<ProcessedExpressionDataVector>	ProcessedExpressionDataVectorDaoImpl.find(Collection<CompositeSequence> designElements, QuantitationType quantitationType)
Collection<ProcessedExpressionDataVector>	ProcessedExpressionDataVectorService.find(Collection<CompositeSequence> designElements, QuantitationType quantitationType)	Retrieve the processed vectors for a set of design elements within a given (processed) quantitation type.
Collection<ProcessedExpressionDataVector>	ProcessedExpressionDataVectorServiceImpl.find(Collection<CompositeSequence> designElements, QuantitationType quantitationType)
Map<ProcessedExpressionDataVector, Collection<Long>>	ProcessedExpressionDataVectorDao.getGenes(Collection<ProcessedExpressionDataVector> vectors)	Obtain the genes associated to each vector.
Map<ProcessedExpressionDataVector, Collection<Long>>	ProcessedExpressionDataVectorDaoImpl.getGenes(Collection<ProcessedExpressionDataVector> vectors)
Collection<ProcessedExpressionDataVector>	ProcessedExpressionDataVectorService.getProcessedDataVectors(ExpressionExperiment expressionExperiment)
Slice<ProcessedExpressionDataVector>	ProcessedExpressionDataVectorService.getProcessedDataVectors(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, int offset, int limit)
Collection<ProcessedExpressionDataVector>	ProcessedExpressionDataVectorServiceImpl.getProcessedDataVectors(ExpressionExperiment expressionExperiment)
Slice<ProcessedExpressionDataVector>	ProcessedExpressionDataVectorServiceImpl.getProcessedDataVectors(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, int offset, int limit)
Collection<ProcessedExpressionDataVector>	ProcessedExpressionDataVectorService.getProcessedDataVectorsAndThaw(ExpressionExperiment expressionExperiment)	Retrieve and thaw a collection of vectors for a given experiment.
Collection<ProcessedExpressionDataVector>	ProcessedExpressionDataVectorServiceImpl.getProcessedDataVectorsAndThaw(ExpressionExperiment expressionExperiment)
Collection<ProcessedExpressionDataVector>	ProcessedExpressionDataVectorDao.getProcessedVectors(ExpressionExperiment expressionExperiment)
List<ProcessedExpressionDataVector>	ProcessedExpressionDataVectorDao.getProcessedVectors(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, int offset, int limit)	Retrieve a slice of processed vectors.
Collection<ProcessedExpressionDataVector>	ProcessedExpressionDataVectorDaoImpl.getProcessedVectors(ExpressionExperiment ee)
List<ProcessedExpressionDataVector>	ProcessedExpressionDataVectorDaoImpl.getProcessedVectors(ExpressionExperiment ee, BioAssayDimension dimension, int offset, int limit)
Map<ProcessedExpressionDataVector, Collection<Long>>	ProcessedExpressionDataVectorDao.getProcessedVectorsAndGenes(Collection<ExpressionExperiment> ees, Map<Long, Collection<Long>> cs2gene)	Obtain processed expression vectors with their associated genes.
Map<ProcessedExpressionDataVector, Collection<Long>>	ProcessedExpressionDataVectorDaoImpl.getProcessedVectorsAndGenes(Collection<ExpressionExperiment> ees, Map<Long, Collection<Long>> cs2gene)
Collection<ProcessedExpressionDataVector>	ProcessedExpressionDataVectorDao.getRandomProcessedVectors(ExpressionExperiment ee, int limit)
Collection<ProcessedExpressionDataVector>	ProcessedExpressionDataVectorDaoImpl.getRandomProcessedVectors(ExpressionExperiment ee, int limit)	Obtain a random sample of processed vectors for the given experiment.

Method parameters in ubic.gemma.persistence.service.expression.bioAssayData with type arguments of type ProcessedExpressionDataVector

Modifier and Type	Method	Description
Map<ProcessedExpressionDataVector, Collection<Long>>	ProcessedExpressionDataVectorDao.getGenes(Collection<ProcessedExpressionDataVector> vectors)	Obtain the genes associated to each vector.
Map<ProcessedExpressionDataVector, Collection<Long>>	ProcessedExpressionDataVectorDaoImpl.getGenes(Collection<ProcessedExpressionDataVector> vectors)
int	ProcessedExpressionDataVectorService.replaceProcessedDataVectors(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> vectors, boolean updateRanks)	Replace the processed vectors of a EE with the given vectors.
int	ProcessedExpressionDataVectorServiceImpl.replaceProcessedDataVectors(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> vectors, boolean updateRanks)

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

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

Modifier and Type	Method	Description
Collection<ProcessedExpressionDataVector>	ExpressionExperimentDao.getProcessedDataVectors(ExpressionExperiment ee)	Retrieve the processed vector for an experiment.
Collection<ProcessedExpressionDataVector>	ExpressionExperimentDao.getProcessedDataVectors(ExpressionExperiment ee, List<BioAssay> assays)	Retrieve a slice of processed vectors for an experiment.
Collection<ProcessedExpressionDataVector>	ExpressionExperimentDaoImpl.getProcessedDataVectors(ExpressionExperiment ee)
Collection<ProcessedExpressionDataVector>	ExpressionExperimentDaoImpl.getProcessedDataVectors(ExpressionExperiment ee, List<BioAssay> assays)
Optional<Collection<ProcessedExpressionDataVector>>	ExpressionExperimentDataVectorService.getProcessedDataVectors(ExpressionExperiment ee)
Optional<Collection<ProcessedExpressionDataVector>>	ExpressionExperimentDataVectorService.getProcessedDataVectors(ExpressionExperiment ee, List<BioAssay> assays)
Optional<Collection<ProcessedExpressionDataVector>>	ExpressionExperimentDataVectorServiceImpl.getProcessedDataVectors(ExpressionExperiment ee)
Optional<Collection<ProcessedExpressionDataVector>>	ExpressionExperimentDataVectorServiceImpl.getProcessedDataVectors(ExpressionExperiment ee, List<BioAssay> assays)
Optional<Collection<ProcessedExpressionDataVector>>	ExpressionExperimentService.getProcessedDataVectors(ExpressionExperiment ee)
Optional<Collection<ProcessedExpressionDataVector>>	ExpressionExperimentService.getProcessedDataVectors(ExpressionExperiment ee, List<BioAssay> assays)
Optional<Collection<ProcessedExpressionDataVector>>	ExpressionExperimentServiceImpl.getProcessedDataVectors(ExpressionExperiment ee)
Optional<Collection<ProcessedExpressionDataVector>>	ExpressionExperimentServiceImpl.getProcessedDataVectors(ExpressionExperiment ee, List<BioAssay> assays)

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

Modifier and Type	Method	Description
int	ExpressionExperimentDao.createProcessedDataVectors(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> vectors)	Add processed data vectors
int	ExpressionExperimentDaoImpl.createProcessedDataVectors(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> vectors)
int	ExpressionExperimentDataVectorService.createProcessedDataVectors(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> vectors)
int	ExpressionExperimentDataVectorServiceImpl.createProcessedDataVectors(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> vectors)
int	ExpressionExperimentService.createProcessedDataVectors(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> vectors)	Create a new set of processed vectors for an experiment.
int	ExpressionExperimentServiceImpl.createProcessedDataVectors(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> vectors)
int	ExpressionExperimentDao.replaceProcessedDataVectors(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> vectors)	Replace processed data vectors.
int	ExpressionExperimentDaoImpl.replaceProcessedDataVectors(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> vectors)
int	ExpressionExperimentDataVectorService.replaceProcessedDataVectors(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> vectors)
int	ExpressionExperimentDataVectorServiceImpl.replaceProcessedDataVectors(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> vectors)
int	ExpressionExperimentService.replaceProcessedDataVectors(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> vectors)	Replace the processed data vectors for the given experiment.
int	ExpressionExperimentServiceImpl.replaceProcessedDataVectors(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> vectors)