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.preprocess.filter
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.preprocess.filter

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

Modifier and Type	Method	Description
ExpressionDataDoubleMatrix	ExpressionExperimentFilter.getFilteredMatrix(Collection<ProcessedExpressionDataVector> dataVectors)	Provides a ready-to-use expression data matrix that is transformed and filtered.

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(String arrayDesignName, FilterConfig filterConfig, Collection<ProcessedExpressionDataVector> dataVectors)
ExpressionDataDoubleMatrix	ExpressionDataMatrixService.getFilteredMatrix(ExpressionExperiment ee, FilterConfig filterConfig, Collection<ProcessedExpressionDataVector> dataVectors)	Provide a filtered expression data matrix.
ExpressionDataDoubleMatrix	ExpressionDataMatrixServiceImpl.getFilteredMatrix(String arrayDesignName, FilterConfig filterConfig, Collection<ProcessedExpressionDataVector> dataVectors)
ExpressionDataDoubleMatrix	ExpressionDataMatrixServiceImpl.getFilteredMatrix(ExpressionExperiment ee, FilterConfig filterConfig, Collection<ProcessedExpressionDataVector> dataVectors)

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

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

Modifier and Type	Method	Description
Collection<ProcessedExpressionDataVector>	ExpressionDataDoubleMatrix.toProcessedDataVectors()

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

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()

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)