Package ubic.gemma.persistence.service.expression.bioAssayData

Class ProcessedExpressionDataVectorDaoImpl

java.lang.Object

ubic.gemma.persistence.service.AbstractDao<T>

ubic.gemma.persistence.service.expression.bioAssayData.AbstractDesignElementDataVectorDao<ProcessedExpressionDataVector>

ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDaoImpl

All Implemented Interfaces:

BaseDao<ProcessedExpressionDataVector>, DesignElementDataVectorDao<ProcessedExpressionDataVector>, ProcessedExpressionDataVectorDao

@Repository
public class ProcessedExpressionDataVectorDaoImpl
extends AbstractDesignElementDataVectorDao<ProcessedExpressionDataVector>
implements ProcessedExpressionDataVectorDao

Author:

Paul

Nested Class Summary

Nested classes/interfaces inherited from interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDao

ProcessedExpressionDataVectorDao.RankMethod

Field Summary

Fields inherited from class ubic.gemma.persistence.service.AbstractDao

elementClass, log

Constructor Summary

Constructors

Constructor	Description
ProcessedExpressionDataVectorDaoImpl(SessionFactory sessionFactory, ProcessedDataVectorCache processedDataVectorCache)

Method Summary

Modifier and Type	Method	Description
void	clearCache()
Set<ProcessedExpressionDataVector>	createProcessedDataVectors(ExpressionExperiment ee, boolean ignoreQuantitationMismatch)	Populate the processed data for the given experiment.
Collection<DoubleVectorValueObject>	getProcessedDataArrays(Collection<? extends BioAssaySet> expressionExperiments, Collection<Long> genes)
Collection<DoubleVectorValueObject>	getProcessedDataArrays(BioAssaySet expressionExperiment)
Collection<DoubleVectorValueObject>	getProcessedDataArrays(BioAssaySet ee, int limit)
Collection<DoubleVectorValueObject>	getProcessedDataArrays(BioAssaySet expressionExperiment, Collection<Long> genes)
Collection<DoubleVectorValueObject>	getProcessedDataArraysByProbe(Collection<? extends BioAssaySet> ees, Collection<CompositeSequence> probes)
Collection<DoubleVectorValueObject>	getProcessedDataArraysByProbeIds(BioAssaySet ee, Collection<Long> probes)
Collection<ProcessedExpressionDataVector>	getProcessedVectors(ExpressionExperiment ee)
Map<ExpressionExperiment,Map<Gene,Collection<Double>>>	getRanks(Collection<ExpressionExperiment> expressionExperiments, Collection<Gene> genes, ProcessedExpressionDataVectorDao.RankMethod method)
Map<Gene,Collection<Double>>	getRanks(ExpressionExperiment expressionExperiment, Collection<Gene> genes, ProcessedExpressionDataVectorDao.RankMethod method)
Map<CompositeSequence,Double>	getRanks(ExpressionExperiment expressionExperiment, ProcessedExpressionDataVectorDao.RankMethod method)
Map<ExpressionExperiment,Map<Gene,Map<CompositeSequence,Double[]>>>	getRanksByProbe(Collection<ExpressionExperiment> expressionExperiments, Collection<Gene> genes)	Retrieve expression level information for genes in experiments.
void	removeProcessedDataVectors(ExpressionExperiment expressionExperiment)

Methods inherited from class ubic.gemma.persistence.service.expression.bioAssayData.AbstractDesignElementDataVectorDao

find, find, find, findByExpressionExperiment, thaw, thaw

Methods inherited from class ubic.gemma.persistence.service.AbstractDao

countAll, create, create, find, findByProperty, findByPropertyIn, findOneByProperty, findOrCreate, getBatchSize, getElementClass, getIdentifierPropertyName, getSessionFactory, load, load, loadAll, loadReference, loadReference, remove, remove, remove, save, save, update, update

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

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

Methods inherited from interface ubic.gemma.persistence.service.expression.bioAssayData.DesignElementDataVectorDao

find, find, find, findByExpressionExperiment, thaw, thaw

Constructor Detail

ProcessedExpressionDataVectorDaoImpl

@Autowired
public ProcessedExpressionDataVectorDaoImpl(SessionFactory sessionFactory,
                                            ProcessedDataVectorCache processedDataVectorCache)

Method Detail

clearCache

public void clearCache()

Specified by:

clearCache in interface ProcessedExpressionDataVectorDao

createProcessedDataVectors

public Set<ProcessedExpressionDataVector> createProcessedDataVectors(ExpressionExperiment ee,
                                                                     boolean ignoreQuantitationMismatch)
                                                              throws QuantitationMismatchException

Description copied from interface: ProcessedExpressionDataVectorDao

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).

Specified by:

createProcessedDataVectors in interface ProcessedExpressionDataVectorDao

Parameters:

ee - ee

ignoreQuantitationMismatch - 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

getProcessedDataArrays

public Collection<DoubleVectorValueObject> getProcessedDataArrays(BioAssaySet expressionExperiment)

Specified by:

getProcessedDataArrays in interface ProcessedExpressionDataVectorDao

getProcessedDataArrays

public Collection<DoubleVectorValueObject> getProcessedDataArrays(BioAssaySet expressionExperiment,
                                                                  Collection<Long> genes)

Specified by:

getProcessedDataArrays in interface ProcessedExpressionDataVectorDao

getProcessedDataArrays

public Collection<DoubleVectorValueObject> getProcessedDataArrays(BioAssaySet ee,
                                                                  int limit)

Specified by:

getProcessedDataArrays in interface ProcessedExpressionDataVectorDao

getProcessedDataArrays

public Collection<DoubleVectorValueObject> getProcessedDataArrays(Collection<? extends BioAssaySet> expressionExperiments,
                                                                  Collection<Long> genes)

Specified by:

getProcessedDataArrays in interface ProcessedExpressionDataVectorDao

getProcessedDataArraysByProbe

public Collection<DoubleVectorValueObject> getProcessedDataArraysByProbe(Collection<? extends BioAssaySet> ees,
                                                                         Collection<CompositeSequence> probes)

Specified by:

getProcessedDataArraysByProbe in interface ProcessedExpressionDataVectorDao

getProcessedDataArraysByProbeIds

public Collection<DoubleVectorValueObject> getProcessedDataArraysByProbeIds(BioAssaySet ee,
                                                                            Collection<Long> probes)

Specified by:

getProcessedDataArraysByProbeIds in interface ProcessedExpressionDataVectorDao

getProcessedVectors

public Collection<ProcessedExpressionDataVector> getProcessedVectors(ExpressionExperiment ee)

Specified by:

getProcessedVectors in interface ProcessedExpressionDataVectorDao

Parameters:

ee - ee

Returns:

Processed data for the given experiment. NOTE the vectors are thawed before returning.

getRanks

public Map<ExpressionExperiment,Map<Gene,Collection<Double>>> getRanks(Collection<ExpressionExperiment> expressionExperiments,
                                                                                   Collection<Gene> genes,
                                                                                   ProcessedExpressionDataVectorDao.RankMethod method)

Specified by:

getRanks in interface ProcessedExpressionDataVectorDao

getRanks

public Map<Gene,Collection<Double>> getRanks(ExpressionExperiment expressionExperiment,
                                                   Collection<Gene> genes,
                                                   ProcessedExpressionDataVectorDao.RankMethod method)

Specified by:

getRanks in interface ProcessedExpressionDataVectorDao

getRanks

public Map<CompositeSequence,Double> getRanks(ExpressionExperiment expressionExperiment,
                                                    ProcessedExpressionDataVectorDao.RankMethod method)

Specified by:

getRanks in interface ProcessedExpressionDataVectorDao

getRanksByProbe

public Map<ExpressionExperiment,Map<Gene,Map<CompositeSequence,Double[]>>> getRanksByProbe(Collection<ExpressionExperiment> expressionExperiments,
                                                                                                             Collection<Gene> genes)

Description copied from interface: ProcessedExpressionDataVectorDao

Retrieve expression level information for genes in experiments.

Specified by:

getRanksByProbe in interface ProcessedExpressionDataVectorDao

Parameters:

expressionExperiments - expression experiments

genes - genes

Returns:

A map of experiment -> gene -> probe -> array of doubles holding the 1) mean and 2) max expression rank.

removeProcessedDataVectors

public void removeProcessedDataVectors(ExpressionExperiment expressionExperiment)

Specified by:

removeProcessedDataVectors in interface ProcessedExpressionDataVectorDao