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

Packages that use ProcessedExpressionDataVector

Package	Description
ubic.gemma.core.analysis.expression.coexpression.links
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.core.analysis.expression.coexpression.links

Method parameters in ubic.gemma.core.analysis.expression.coexpression.links with type arguments of type ProcessedExpressionDataVector

Modifier and Type	Method	Description
LinkAnalysis	LinkAnalysisService.processVectors(Taxon t, Collection<ProcessedExpressionDataVector> dataVectors, FilterConfig filterConfig, LinkAnalysisConfig linkAnalysisConfig)	Used when the input is data vectors from another source, instead of from a DB-bound expressionExperiment.
LinkAnalysis	LinkAnalysisServiceImpl.processVectors(Taxon t, Collection<ProcessedExpressionDataVector> dataVectors, FilterConfig filterConfig, LinkAnalysisConfig linkAnalysisConfig)

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, FilterConfig filterConfig, boolean logTransform)
ExpressionDataDoubleMatrix	ExpressionDataMatrixService.getFilteredMatrix(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> dataVectors, FilterConfig filterConfig, boolean logTransform)	Provide a filtered expression data matrix.
ExpressionDataDoubleMatrix	ExpressionDataMatrixServiceImpl.getFilteredMatrix(Collection<ProcessedExpressionDataVector> dataVectors, ArrayDesign arrayDesign, FilterConfig filterConfig, boolean logTransform)
ExpressionDataDoubleMatrix	ExpressionDataMatrixServiceImpl.getFilteredMatrix(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> dataVectors, FilterConfig filterConfig, boolean logTransform)

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)

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

Methods in ubic.gemma.persistence.service.expression.bioAssayData that return types with 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)
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>>	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	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	ExpressionExperimentService.replaceProcessedDataVectors(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> vectors)	Replace the processed data vectors for the given experiment.
int	ExpressionExperimentServiceImpl.replaceProcessedDataVectors(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> vectors)