Interface ProcessedExpressionDataVectorDao
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- All Superinterfaces:
BaseDao<ProcessedExpressionDataVector>
,DesignElementDataVectorDao<ProcessedExpressionDataVector>
- All Known Implementing Classes:
ProcessedExpressionDataVectorDaoImpl
public interface ProcessedExpressionDataVectorDao extends DesignElementDataVectorDao<ProcessedExpressionDataVector>
- Author:
- Paul
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Nested Class Summary
Nested Classes Modifier and Type Interface Description static class
ProcessedExpressionDataVectorDao.RankMethod
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Method Summary
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Methods inherited from interface ubic.gemma.persistence.service.BaseDao
countAll, create, create, find, findOrCreate, getElementClass, getIdentifierPropertyName, load, load, loadAll, loadReference, loadReference, remove, remove, remove, save, save, update, update
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Methods inherited from interface ubic.gemma.persistence.service.expression.bioAssayData.DesignElementDataVectorDao
find, find, find, findByExpressionExperiment, thaw, thaw
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Method Detail
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clearCache
void clearCache()
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createProcessedDataVectors
Set<ProcessedExpressionDataVector> createProcessedDataVectors(ExpressionExperiment expressionExperiment, boolean ignoreQuantitationMismatch) throws QuantitationMismatchException
Populate the processed data for the given experiment. For two-channel studies, the missing value information should already have been computed. If the values already exist, they will be re-written. The data will be quantile normalized (with some exceptions: ratios and count data will not be normalized).- Parameters:
expressionExperiment
- eeignoreQuantitationMismatch
- use raw data to infer scale type and the adequate transformation for producing processed EVs instead of relying on the QT- Returns:
- the created processed vectors
- Throws:
QuantitationMismatchException
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getProcessedDataArrays
Collection<DoubleVectorValueObject> getProcessedDataArrays(BioAssaySet expressionExperiment)
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getProcessedDataArrays
Collection<DoubleVectorValueObject> getProcessedDataArrays(BioAssaySet expressionExperiment, Collection<Long> genes)
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getProcessedDataArrays
Collection<DoubleVectorValueObject> getProcessedDataArrays(BioAssaySet expressionExperiment, int limit)
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getProcessedDataArrays
Collection<DoubleVectorValueObject> getProcessedDataArrays(Collection<? extends BioAssaySet> expressionExperiments, Collection<Long> genes)
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getProcessedDataArraysByProbe
Collection<DoubleVectorValueObject> getProcessedDataArraysByProbe(Collection<? extends BioAssaySet> expressionExperiments, Collection<CompositeSequence> probes)
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getProcessedDataArraysByProbeIds
Collection<DoubleVectorValueObject> getProcessedDataArraysByProbeIds(BioAssaySet ee, Collection<Long> probes)
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getProcessedVectors
Collection<ProcessedExpressionDataVector> getProcessedVectors(ExpressionExperiment expressionExperiment)
- Parameters:
expressionExperiment
- ee- Returns:
- Processed data for the given experiment. NOTE the vectors are thawed before returning.
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getRanks
Map<ExpressionExperiment,Map<Gene,Collection<Double>>> getRanks(Collection<ExpressionExperiment> expressionExperiments, Collection<Gene> genes, ProcessedExpressionDataVectorDao.RankMethod method)
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getRanks
Map<Gene,Collection<Double>> getRanks(ExpressionExperiment expressionExperiment, Collection<Gene> genes, ProcessedExpressionDataVectorDao.RankMethod method)
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getRanks
Map<CompositeSequence,Double> getRanks(ExpressionExperiment expressionExperiment, ProcessedExpressionDataVectorDao.RankMethod method)
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getRanksByProbe
Map<ExpressionExperiment,Map<Gene,Map<CompositeSequence,Double[]>>> getRanksByProbe(Collection<ExpressionExperiment> expressionExperiments, Collection<Gene> genes)
Retrieve expression level information for genes in experiments.- Parameters:
genes
- genesexpressionExperiments
- expression experiments- Returns:
- A map of experiment -> gene -> probe -> array of doubles holding the 1) mean and 2) max expression rank.
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removeProcessedDataVectors
void removeProcessedDataVectors(ExpressionExperiment expressionExperiment)
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