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

Interface ProcessedExpressionDataVectorService

All Superinterfaces:

BaseReadOnlyService<ProcessedExpressionDataVector>

All Known Implementing Classes:

ProcessedExpressionDataVectorServiceImpl

public interface ProcessedExpressionDataVectorService

Author:

Paul

Method Summary

Modifier and Type	Method	Description
int	createProcessedDataVectors(ExpressionExperiment expressionExperiment, boolean updateRanks)	Create processed vectors and optionally update ranks.
int	createProcessedDataVectors(ExpressionExperiment expressionExperiment, boolean updateRanks, boolean ignoreQuantitationMismatch)	Create processed vectors and optionally update ranks.
void	evictFromCache(ExpressionExperiment ee)
Collection<T>	find(Collection<QuantitationType> quantitationTypes)	Find specific type (DesignElementDataVectorService) of vectors that meet the given criteria.
Collection<T>	find(QuantitationType quantitationType)	Find specific type (DesignElementDataVectorService) 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>	findAndThaw(Collection<QuantitationType> quantitationTypes)
Collection<T>	findAndThaw(QuantitationType quantitationType)	Find and thaw specific type (DesignElementDataVectorService) of vectors that meet the given criteria.
Collection<T>	findAndThaw(BioAssayDimension bioAssayDimension)
List<DoubleVectorValueObject>	getDiffExVectors(Long resultSetId, double threshold, int maxNumberOfResults)
List<ExperimentExpressionLevelsValueObject>	getExpressionLevels(Collection<ExpressionExperiment> ees, Collection<Gene> genes, boolean keepGeneNonSpecific, String consolidateMode)
List<ExperimentExpressionLevelsValueObject>	getExpressionLevelsByIds(Collection<Long> datasetIds, Collection<Gene> genes, boolean keepNonSpecific, String consolidationMode)	Retrieve expression levels by dataset IDs.
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<ExpressionExperiment> expressionExperiments, Collection<Long> genes)
Collection<DoubleVectorValueObject>	getProcessedDataArrays(BioAssaySet bioAssaySet, Collection<Long> genes)
Collection<DoubleVectorValueObject>	getProcessedDataArrays(ExpressionExperiment expressionExperiment)
Collection<DoubleVectorValueObject>	getProcessedDataArraysByProbe(Collection<ExpressionExperiment> expressionExperiments, Collection<CompositeSequence> compositeSequences)
Collection<DoubleVectorValueObject>	getProcessedDataArraysByProbe(ExpressionExperiment ee, Collection<CompositeSequence> compositeSequences)
Collection<ProcessedExpressionDataVector>	getProcessedDataVectors(ExpressionExperiment expressionExperiment)
Slice<ProcessedExpressionDataVector>	getProcessedDataVectors(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, int offset, int limit)
Collection<ProcessedExpressionDataVector>	getProcessedDataVectorsAndThaw(ExpressionExperiment expressionExperiment)	Retrieve and thaw a collection of vectors for a given experiment.
Slice<CompositeSequence>	getProcessedDataVectorsDesignElements(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, int offset, int limit)
Collection<DoubleVectorValueObject>	getRandomProcessedDataArrays(ExpressionExperiment ee, int limit)
Map<ExpressionExperiment,Map<Gene,Collection<Double>>>	getRanks(Collection<ExpressionExperiment> expressionExperiments, Collection<Gene> genes, ProcessedExpressionDataVectorDao.RankMethod method)
int	removeProcessedDataVectors(ExpressionExperiment ee)	Remove the processed vectors of an EE.
void	reorderByDesign(ExpressionExperiment ee)	Creates new bioAssayDimensions to match the experimental design, reorders the data to match, updates.
int	replaceProcessedDataVectors(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> vectors, boolean updateRanks)	Replace the processed vectors of a EE with the given vectors.
Collection<T>	thaw(Collection<T> vectors)	Deprecated. Use findAndThaw(QuantitationType), findAndThaw(Collection) or findAndThaw(BioAssayDimension) instead, it's much more efficient.
void	updateRanks(ExpressionExperiment ee)	Update the ranks of the processed vectors for the given experiment.

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

countAll, find, findOrFail, getElementClass, load, load, loadAll, loadOrFail, loadOrFail, loadOrFail, loadOrFail, streamAll, streamAll

Method Detail

createProcessedDataVectors

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
int createProcessedDataVectors(ExpressionExperiment expressionExperiment,
                               boolean updateRanks)
                        throws QuantitationTypeConversionException

Create processed vectors and optionally update ranks.

Mismatch between quantitation type and data is ignored.

This also adds an audit event and evict the vectors from the cache.

Parameters:

updateRanks - whether to update the rnaks of the vectors or not

Throws:

QuantitationTypeConversionException - if the data cannot be converted, generally to log2 scale

See Also:

updateRanks(ExpressionExperiment), ProcessedExpressionDataVectorDao.createProcessedDataVectors(ExpressionExperiment, boolean)

createProcessedDataVectors

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
int createProcessedDataVectors(ExpressionExperiment expressionExperiment,
                               boolean updateRanks,
                               boolean ignoreQuantitationMismatch)
                        throws QuantitationTypeDetectionException,
                               QuantitationTypeConversionException

Create processed vectors and optionally update ranks.

This also adds an audit event and evict the vectors from the cache.

Throws:

QuantitationTypeDetectionException - if the QT caanot be detected from data, never raised if ignoreQuantitationMismatch is set to true

QuantitationTypeConversionException - if the data cannot be converted, generally to log2 scale

See Also:

createProcessedDataVectors(ExpressionExperiment, boolean), updateRanks(ExpressionExperiment)

replaceProcessedDataVectors

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
int replaceProcessedDataVectors(ExpressionExperiment ee,
                                Collection<ProcessedExpressionDataVector> vectors,
                                boolean updateRanks)

Replace the processed vectors of a EE with the given vectors.

Ranks are recomputed, no conversion of QT is done.

This also adds an audit event and evict the vectors from the cache.

Parameters:

ee - ee

vectors - non-persistent, all of the same QuantitationType

updateRanks - whether to update ranks or not

See Also:

ProcessedExpressionDataVectorDao.createProcessedDataVectors(ExpressionExperiment, boolean)

removeProcessedDataVectors

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
int removeProcessedDataVectors(ExpressionExperiment ee)

Remove the processed vectors of an EE.

This also adds an audit event and evict the vectors from the cache.

See Also:

ExpressionExperimentService.removeProcessedDataVectors(ExpressionExperiment)

reorderByDesign

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
void reorderByDesign(ExpressionExperiment ee)

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

This also adds an audit event and evict the vectors from the cache.

updateRanks

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
void updateRanks(ExpressionExperiment ee)

Update the ranks of the processed vectors for the given experiment.

This also adds an audit event and evict the vectors from the cache.

getExpressionLevels

@Secured({"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

getExpressionLevelsByIds

@Secured("IS_AUTHENTICATED_ANONYMOUSLY")
List<ExperimentExpressionLevelsValueObject> getExpressionLevelsByIds(Collection<Long> datasetIds,
                                                                     Collection<Gene> genes,
                                                                     boolean keepNonSpecific,
                                                                     @Nullable
                                                                     String consolidationMode)

Retrieve expression levels by dataset IDs.

See Also:

getExpressionLevels(Collection, Collection, boolean, String)

getExpressionLevelsPca

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_COLLECTION_READ"})
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({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_COLLECTION_READ"})
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({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_COLLECTION_READ"})
Collection<DoubleVectorValueObject> getProcessedDataArrays(Collection<ExpressionExperiment> expressionExperiments,
                                                           Collection<Long> genes)

See Also:

CachedProcessedExpressionDataVectorService.getProcessedDataArrays(Collection, Collection)

getProcessedDataArrays

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Collection<DoubleVectorValueObject> getProcessedDataArrays(BioAssaySet bioAssaySet,
                                                           Collection<Long> genes)

See Also:

CachedProcessedExpressionDataVectorService.getProcessedDataArrays(BioAssaySet, Collection)

getProcessedDataArrays

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

See Also:

CachedProcessedExpressionDataVectorService.getProcessedDataArrays(BioAssaySet)

getRandomProcessedDataArrays

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

See Also:

CachedProcessedExpressionDataVectorService.getRandomProcessedDataArrays(BioAssaySet, int)

getProcessedDataArraysByProbe

Collection<DoubleVectorValueObject> getProcessedDataArraysByProbe(ExpressionExperiment ee,
                                                                  Collection<CompositeSequence> compositeSequences)

getProcessedDataArraysByProbe

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_COLLECTION_READ"})
Collection<DoubleVectorValueObject> getProcessedDataArraysByProbe(Collection<ExpressionExperiment> expressionExperiments,
                                                                  Collection<CompositeSequence> compositeSequences)

See Also:

CachedProcessedExpressionDataVectorService.getProcessedDataArraysByProbe(Collection, Collection)

getProcessedDataVectors

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Collection<ProcessedExpressionDataVector> getProcessedDataVectors(ExpressionExperiment expressionExperiment)

See Also:

ProcessedExpressionDataVectorDao.getProcessedVectors(ExpressionExperiment)

getProcessedDataVectors

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Slice<ProcessedExpressionDataVector> getProcessedDataVectors(ExpressionExperiment expressionExperiment,
                                                             BioAssayDimension dimension,
                                                             int offset,
                                                             int limit)

getProcessedDataVectorsDesignElements

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Slice<CompositeSequence> getProcessedDataVectorsDesignElements(ExpressionExperiment expressionExperiment,
                                                               BioAssayDimension dimension,
                                                               int offset,
                                                               int limit)

getProcessedDataVectorsAndThaw

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Collection<ProcessedExpressionDataVector> getProcessedDataVectorsAndThaw(ExpressionExperiment expressionExperiment)

Retrieve and thaw a collection of vectors for a given experiment.

See Also:

ProcessedExpressionDataVectorDao.getProcessedVectors(ExpressionExperiment), DesignElementDataVectorDao.thaw(Collection)

getRanks

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

See Also:

ProcessedExpressionDataVectorDao.getRanks(ExpressionExperiment, Collection, ProcessedExpressionDataVectorDao.RankMethod)

getDiffExVectors

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

evictFromCache

void evictFromCache(ExpressionExperiment ee)

find

@Secured({"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 DesignElementDataVectorService

findAndThaw

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

find

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

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

Parameters:

quantitationTypes - the QTs

Returns:

the found vectors of type DesignElementDataVectorService

findAndThaw

@Secured("GROUP_ADMIN")
Collection<T> findAndThaw(Collection<QuantitationType> quantitationTypes)

find

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

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

Parameters:

quantitationType - the QT

Returns:

the found vectors of type DesignElementDataVectorService

findAndThaw

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

Find and thaw specific type (DesignElementDataVectorService) of vectors that meet the given criteria.

thaw

@CheckReturnValue
@Deprecated
Collection<T> thaw(Collection<T> vectors)

Deprecated.

Use findAndThaw(QuantitationType), findAndThaw(Collection) or findAndThaw(BioAssayDimension) instead, it's much more efficient.

Thaw the given vectors.