ubic.gemma.persistence.service.expression.bioAssayData

Interface ProcessedExpressionDataVectorService

All Known Implementing Classes:

ProcessedExpressionDataVectorServiceImpl

public interface ProcessedExpressionDataVectorService

Author:

Paul

Method Summary

Modifier and Type	Method and Description
void	clearCache()
Collection<ProcessedExpressionDataVector>	computeProcessedExpressionData(ExpressionExperiment ee) This method should not be called on its own, if possible.
ExpressionExperiment	createProcessedDataVectors(ExpressionExperiment expressionExperiment) Populate the processed data for the given experiment.
ExpressionExperiment	createProcessedDataVectors(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> vectors)
Collection<T>	find(ArrayDesign arrayDesign, QuantitationType quantitationType) Find specific type (T) of vectors that meet the given criteria.
Collection<T>	find(BioAssayDimension bioAssayDimension) Find specific type (raw or processed, depending on the service) of vectors that meet the given criteria.
Collection<T>	find(Collection<CompositeSequence> designElements, QuantitationType quantitationType) Find specific type (T) of vectors that meet the given criteria.
Collection<T>	find(Collection<QuantitationType> quantitationTypes) Find specific type (T) of vectors that meet the given criteria.
Collection<T>	find(QuantitationType quantitationType) Find specific type (T) of vectors that meet the given criteria.
Collection<T>	findByExpressionExperiment(ExpressionExperiment expressionExperiment, QuantitationType quantitationType)
Collection<DesignElementDataVector>	findRawAndProcessed(BioAssayDimension dim) Finds all vectors for the given BA Dimension
Collection<DesignElementDataVector>	findRawAndProcessed(QuantitationType qt) Finds all vectors for the given quantitation type
List<DoubleVectorValueObject>	getDiffExVectors(Long resultSetId, Double threshold, int maxNumberOfResults)
List<ExperimentExpressionLevelsValueObject>	getExpressionLevels(Collection<ExpressionExperiment> ees, Collection<Gene> genes, boolean keepGeneNonSpecific, String consolidateMode)
List<ExperimentExpressionLevelsValueObject>	getExpressionLevelsDiffEx(Collection<ExpressionExperiment> ees, Long diffExResultSetId, double threshold, int max, boolean keepGeneNonSpecific, String consolidateMode)
List<ExperimentExpressionLevelsValueObject>	getExpressionLevelsPca(Collection<ExpressionExperiment> ees, int threshold, int component, boolean keepGeneNonSpecific, String consolidateMode)
Collection<DoubleVectorValueObject>	getProcessedDataArrays(Collection<? extends BioAssaySet> bioassaySets, Collection<Long> genes)
Collection<DoubleVectorValueObject>	getProcessedDataArrays(ExpressionExperiment expressionExperiment)
Collection<DoubleVectorValueObject>	getProcessedDataArrays(ExpressionExperiment ee, int limit)
Collection<DoubleVectorValueObject>	getProcessedDataArraysByProbe(Collection<? extends BioAssaySet> expressionExperiments, Collection<CompositeSequence> compositeSequences) Retrieves DEDV's by probes and experiments
Collection<DoubleVectorValueObject>	getProcessedDataArraysByProbeIds(BioAssaySet analyzedSet, Collection<Long> probes)
Collection<ProcessedExpressionDataVector>	getProcessedDataVectors(ExpressionExperiment expressionExperiment)
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> eeCol, Collection<Gene> pars) Retrieve expression level information for genes in experiments.
void	remove(Collection<ProcessedExpressionDataVector> processedExpressionDataVectors) Deprecated. never use this method, you can use removeProcessedDataVectors(ExpressionExperiment) instead, or clear ExpressionExperiment.getProcessedExpressionDataVectors() directly. The relationship is actually managed by Hibernate.
void	removeDataForCompositeSequence(CompositeSequence compositeSequence) Removes specific type (T) of vectors for the given CS.
void	removeDataForQuantitationType(QuantitationType quantitationType) Removes specific type (T) of vectors for the given QT.
void	removeProcessedDataVectors(ExpressionExperiment expressionExperiment)
void	reorderByDesign(Long eeId) Creates new bioAssayDimensions to match the experimental design, reorders the data to match, updates.
void	thaw(Collection<T> designElementDataVectors) Thaws the given vectors.
void	thawRawAndProcessed(Collection<DesignElementDataVector> vectors) Thaws all data vectors in the given collection
void	update(T dedv) Updates the given entity in the persistent storage.

Methods inherited from interface ubic.gemma.persistence.service.BaseService

countAll, create, create, find, findOrCreate, findOrFail, load, load, loadAll, loadOrFail, remove, remove, removeAll, save, save, update

Method Detail

createProcessedDataVectors

@Secured(value="GROUP_USER")
ExpressionExperiment createProcessedDataVectors(ExpressionExperiment ee,
                                                                             Collection<ProcessedExpressionDataVector> vectors)

Parameters:

ee - ee

vectors - non-persistent, all of the same quantitationtype

Returns:

ee

clearCache

@Secured(value="GROUP_ADMIN")
void clearCache()

createProcessedDataVectors

@Secured(value="GROUP_USER")
ExpressionExperiment createProcessedDataVectors(ExpressionExperiment expressionExperiment)

Populate the processed data for the given experiment. For two-channel studies, the missing value information should already have been computed.

Parameters:

expressionExperiment - ee

Returns:

updated expressionExperiment

getProcessedDataArrays

@Secured(value={"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_COLLECTION_READ"})
Collection<DoubleVectorValueObject> getProcessedDataArrays(Collection<? extends BioAssaySet> bioassaySets,
                                                                                                                                            Collection<Long> genes)

Parameters:

bioassaySets - - expressionExperiments or expressionExperimentSubSets

genes - genes

Returns:

vectors, which will be subsetted if the bioassayset is a subset.

getExpressionLevels

@Secured(value={"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_COLLECTION_READ"})
List<ExperimentExpressionLevelsValueObject> getExpressionLevels(Collection<ExpressionExperiment> ees,
                                                                                                                                                 Collection<Gene> genes,
                                                                                                                                                 boolean keepGeneNonSpecific,
                                                                                                                                                 @Nullable
                                                                                                                                                 String consolidateMode)

Parameters:

ees - expressionExperiments

genes - genes

consolidateMode - how to consolidate the vectors when there is more than one

keepGeneNonSpecific - whether to keep vectors that are not specific to the gene

Returns:

value objects containing structured information about the expression levels of given genes

getExpressionLevelsPca

@Secured(value={"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_COLLECTION_READ"})
 @Transactional(readOnly=true)
List<ExperimentExpressionLevelsValueObject> getExpressionLevelsPca(Collection<ExpressionExperiment> ees,
                                                                                                                                                                                   int threshold,
                                                                                                                                                                                   int component,
                                                                                                                                                                                   boolean keepGeneNonSpecific,
                                                                                                                                                                                   @Nullable
                                                                                                                                                                                   String consolidateMode)

Parameters:

ees - expressionExperiments

component - the principal component

threshold - threshold

consolidateMode - how to consolidate the vectors when there is more than one

keepGeneNonSpecific - whether to keep vectors that are not specific to the gene

Returns:

value objects containing structured information about the expression levels of genes highly loaded in the given principal component.

getExpressionLevelsDiffEx

@Secured(value={"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_COLLECTION_READ"})
 @Transactional(readOnly=true)
List<ExperimentExpressionLevelsValueObject> getExpressionLevelsDiffEx(Collection<ExpressionExperiment> ees,
                                                                                                                                                                                      Long diffExResultSetId,
                                                                                                                                                                                      double threshold,
                                                                                                                                                                                      int max,
                                                                                                                                                                                      boolean keepGeneNonSpecific,
                                                                                                                                                                                      @Nullable
                                                                                                                                                                                      String consolidateMode)

Parameters:

diffExResultSetId - the differential expression result set to access

threshold - threshold

consolidateMode - how to consolidate the vectors when there is more than one

keepGeneNonSpecific - whether to keep vectors that are not specific to the gene

ees - ees

max - max level

Returns:

value objects containing structured information about the expression levels of genes highly loaded in the given principal component.

getProcessedDataArrays

@Secured(value={"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Collection<DoubleVectorValueObject> getProcessedDataArrays(ExpressionExperiment expressionExperiment)

Parameters:

expressionExperiment - ee

Returns:

double vector vos

getProcessedDataArrays

@Secured(value={"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Collection<DoubleVectorValueObject> getProcessedDataArrays(ExpressionExperiment ee,
                                                                                                                                 int limit)

Parameters:

limit - (null limit = default hibernate limit).

ee - ee

Returns:

double vector vos

getProcessedDataArraysByProbe

@Secured(value={"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_COLLECTION_READ"})
Collection<DoubleVectorValueObject> getProcessedDataArraysByProbe(Collection<? extends BioAssaySet> expressionExperiments,
                                                                                                                                                   Collection<CompositeSequence> compositeSequences)

Retrieves DEDV's by probes and experiments

Parameters:

expressionExperiments - EEs

compositeSequences - composite sequences

Returns:

double vector vos

getProcessedDataArraysByProbeIds

@Secured(value={"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Collection<DoubleVectorValueObject> getProcessedDataArraysByProbeIds(BioAssaySet analyzedSet,
                                                                                                                                           Collection<Long> probes)

getProcessedDataVectors

Collection<ProcessedExpressionDataVector> getProcessedDataVectors(ExpressionExperiment expressionExperiment)

getRanks

@Secured(value={"IS_AUTHENTICATED_ANONYMOUSLY","ACL_AFTER_MAP_READ","ACL_SECURABLE_COLLECTION_READ"})
Map<ExpressionExperiment,Map<Gene,Collection<Double>>> getRanks(Collection<ExpressionExperiment> expressionExperiments,
                                                                                                                                                                      Collection<Gene> genes,
                                                                                                                                                                      ProcessedExpressionDataVectorDao.RankMethod method)

getRanks

@Secured(value={"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Map<Gene,Collection<Double>> getRanks(ExpressionExperiment expressionExperiment,
                                                                                                            Collection<Gene> genes,
                                                                                                            ProcessedExpressionDataVectorDao.RankMethod method)

getRanks

@Secured(value={"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Map<CompositeSequence,Double> getRanks(ExpressionExperiment expressionExperiment,
                                                                                                             ProcessedExpressionDataVectorDao.RankMethod method)

getRanksByProbe

@Secured(value={"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_COLLECTION_READ"})
Map<ExpressionExperiment,Map<Gene,Map<CompositeSequence,Double[]>>> getRanksByProbe(Collection<ExpressionExperiment> eeCol,
                                                                                                                                                                     Collection<Gene> pars)

Retrieve expression level information for genes in experiments.

Parameters:

eeCol - ees

pars - genes

Returns:

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

removeProcessedDataVectors

@Secured(value={"GROUP_USER","ACL_SECURABLE_EDIT"})
void removeProcessedDataVectors(ExpressionExperiment expressionExperiment)

remove

@Deprecated
void remove(Collection<ProcessedExpressionDataVector> processedExpressionDataVectors)

Deprecated. never use this method, you can use removeProcessedDataVectors(ExpressionExperiment) instead, or clear ExpressionExperiment.getProcessedExpressionDataVectors() directly. The relationship is actually managed by Hibernate.

Description copied from interface: BaseService

Removes all the given entities from persistent storage.

Parameters:

processedExpressionDataVectors - the entities to be removed.

getDiffExVectors

List<DoubleVectorValueObject> getDiffExVectors(Long resultSetId,
                                               Double threshold,
                                               int maxNumberOfResults)

computeProcessedExpressionData

@Secured(value="GROUP_ADMIN")
Collection<ProcessedExpressionDataVector> computeProcessedExpressionData(ExpressionExperiment ee)

This method should not be called on its own, if possible. Use the PreprocessorService to do all necessary refreshing.

Parameters:

ee - the experiment

Returns:

processed data vectors

See Also:

PreprocessorService

reorderByDesign

@Secured(value="GROUP_ADMIN")
void reorderByDesign(Long eeId)

Creates new bioAssayDimensions to match the experimental design, reorders the data to match, updates.

Parameters:

eeId - the experiment id

thawRawAndProcessed

@Secured(value="GROUP_ADMIN")
void thawRawAndProcessed(Collection<DesignElementDataVector> vectors)

Thaws all data vectors in the given collection

Parameters:

vectors - the vectors to be thawed

findRawAndProcessed

@Secured(value="GROUP_ADMIN")
Collection<DesignElementDataVector> findRawAndProcessed(BioAssayDimension dim)

Finds all vectors for the given BA Dimension

Parameters:

dim - the BA dimension to limit the vector search to

Returns:

the found data vectors

findRawAndProcessed

@Secured(value="GROUP_ADMIN")
Collection<DesignElementDataVector> findRawAndProcessed(QuantitationType qt)

Finds all vectors for the given quantitation type

Parameters:

qt - the quantitation type to limit the vector search to

Returns:

the found data vectors

removeDataForCompositeSequence

@Secured(value="GROUP_ADMIN")
void removeDataForCompositeSequence(CompositeSequence compositeSequence)

Removes specific type (T) of vectors for the given CS.

Parameters:

compositeSequence - the sequence to remove the data for.

removeDataForQuantitationType

@Secured(value="GROUP_ADMIN")
void removeDataForQuantitationType(QuantitationType quantitationType)

Removes specific type (T) of vectors for the given QT.

Parameters:

quantitationType - the QT to remove the data for.

thaw

void thaw(Collection<T> designElementDataVectors)

Thaws the given vectors.

Parameters:

designElementDataVectors - the vectors to thaw.

find

@Secured(value={"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_DATAVECTOR_COLLECTION_READ"})
Collection<T> find(ArrayDesign arrayDesign,
                                                                                                           QuantitationType quantitationType)

Find specific type (T) of vectors that meet the given criteria.

Parameters:

arrayDesign - the AD

quantitationType - the QT

Returns:

the found vectors of type T.

find

@Secured(value={"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_DATAVECTOR_COLLECTION_READ"})
Collection<T> find(BioAssayDimension bioAssayDimension)

Find specific type (raw or processed, depending on the service) of vectors that meet the given criteria.

Parameters:

bioAssayDimension - the BA dimension

Returns:

the found vectors of type T

find

@Secured(value="GROUP_ADMIN")
Collection<T> find(Collection<QuantitationType> quantitationTypes)

Find specific type (T) of vectors that meet the given criteria.

Parameters:

quantitationTypes - the QTs

Returns:

the found vectors of type T

find

@Secured(value={"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_DATAVECTOR_COLLECTION_READ"})
Collection<T> find(QuantitationType quantitationType)

Find specific type (T) of vectors that meet the given criteria.

Parameters:

quantitationType - the QT

Returns:

the found vectors of type T

find

@Secured(value={"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_DATAVECTOR_COLLECTION_READ"})
Collection<T> find(Collection<CompositeSequence> designElements,
                                                                                                           QuantitationType quantitationType)

Find specific type (T) of vectors that meet the given criteria.

Parameters:

designElements - design elements

quantitationType - the QT

Returns:

the found vectors of type T

findByExpressionExperiment

@Secured(value={"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_DATAVECTOR_COLLECTION_READ"})
Collection<T> findByExpressionExperiment(ExpressionExperiment expressionExperiment,
                                                                                                                                 QuantitationType quantitationType)

See Also:

DesignElementDataVectorDao.findByExpressionExperiment(ExpressionExperiment, QuantitationType)

update

@Secured(value="GROUP_USER")
void update(T dedv)

Description copied from interface: BaseService

Updates the given entity in the persistent storage.

Specified by:

update in interface BaseService<T extends DesignElementDataVector>

Parameters:

dedv - the entity to be updated.