Uses of Class
ubic.gemma.model.expression.bioAssayData.ProcessedExpressionDataVector
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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)
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Uses of ProcessedExpressionDataVector in ubic.gemma.core.analysis.preprocess
Constructor parameters in ubic.gemma.core.analysis.preprocess with type arguments of type ProcessedExpressionDataVector Constructor Description ExpressionDataMatrixBuilder(Collection<ProcessedExpressionDataVector> processedVectors, Collection<? extends DesignElementDataVector> otherVectors)
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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)
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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()
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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()
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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)
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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 Set<ProcessedExpressionDataVector>
ProcessedExpressionDataVectorDao. createProcessedDataVectors(ExpressionExperiment expressionExperiment, boolean ignoreQuantitationMismatch)
Populate the processed data for the given experiment.Set<ProcessedExpressionDataVector>
ProcessedExpressionDataVectorDaoImpl. createProcessedDataVectors(ExpressionExperiment ee, boolean ignoreQuantitationMismatch)
Set<ProcessedExpressionDataVector>
ProcessedExpressionDataVectorService. createProcessedDataVectors(ExpressionExperiment expressionExperiment)
Set<ProcessedExpressionDataVector>
ProcessedExpressionDataVectorService. createProcessedDataVectors(ExpressionExperiment expressionExperiment, boolean ignoreInferredScale)
Populate the processed data for the given experiment.Set<ProcessedExpressionDataVector>
ProcessedExpressionDataVectorServiceImpl. createProcessedDataVectors(ExpressionExperiment expressionExperiment)
Set<ProcessedExpressionDataVector>
ProcessedExpressionDataVectorServiceImpl. createProcessedDataVectors(ExpressionExperiment expressionExperiment, boolean ignoreQuantitationMismatch)
Collection<ProcessedExpressionDataVector>
ProcessedExpressionDataVectorService. getProcessedDataVectors(ExpressionExperiment expressionExperiment)
Collection<ProcessedExpressionDataVector>
ProcessedExpressionDataVectorServiceImpl. getProcessedDataVectors(ExpressionExperiment expressionExperiment)
Collection<ProcessedExpressionDataVector>
ProcessedExpressionDataVectorService. getProcessedDataVectorsAndThaw(ExpressionExperiment expressionExperiment)
Collection<ProcessedExpressionDataVector>
ProcessedExpressionDataVectorServiceImpl. getProcessedDataVectorsAndThaw(ExpressionExperiment expressionExperiment)
Collection<ProcessedExpressionDataVector>
ProcessedExpressionDataVectorDao. getProcessedVectors(ExpressionExperiment expressionExperiment)
Collection<ProcessedExpressionDataVector>
ProcessedExpressionDataVectorDaoImpl. getProcessedVectors(ExpressionExperiment ee)
Method parameters in ubic.gemma.persistence.service.expression.bioAssayData with type arguments of type ProcessedExpressionDataVector Modifier and Type Method Description void
ProcessedExpressionDataVectorService. replaceProcessedDataVectors(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> vectors)
Replace the processed vectors of a EE with the given vectors.void
ProcessedExpressionDataVectorServiceImpl. replaceProcessedDataVectors(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> vectors)
void
ProcessedExpressionDataVectorService. update(Collection<ProcessedExpressionDataVector> updatedVectors)
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