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
void	clearCache()
void	computeProcessedExpressionData(ExpressionExperiment ee)	Compute processed expression data, ignoring mismatched with the inferred scale.
void	computeProcessedExpressionData(ExpressionExperiment ee, boolean ignoreInferredScale)	This method should not be called on its own, if possible.
Set<ProcessedExpressionDataVector>	createProcessedDataVectors(ExpressionExperiment expressionExperiment)
Set<ProcessedExpressionDataVector>	createProcessedDataVectors(ExpressionExperiment expressionExperiment, boolean ignoreInferredScale)	Populate the processed data for the given experiment.
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)
Collection<ProcessedExpressionDataVector>	findByExpressionExperiment(ExpressionExperiment ee, QuantitationType quantitationType)
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<ExpressionExperiment> expressionExperiments, Collection<Long> genes)
Collection<DoubleVectorValueObject>	getProcessedDataArrays(BioAssaySet ee, Collection<Long> genes)
Collection<DoubleVectorValueObject>	getProcessedDataArrays(ExpressionExperiment expressionExperiment)
Collection<DoubleVectorValueObject>	getProcessedDataArrays(ExpressionExperiment ee, int limit)
Collection<DoubleVectorValueObject>	getProcessedDataArraysByProbe(Collection<ExpressionExperiment> expressionExperiments, Collection<CompositeSequence> compositeSequences)	Retrieves DEDV's by probes and experiments
Collection<DoubleVectorValueObject>	getProcessedDataArraysByProbeIds(BioAssaySet analyzedSet, Collection<Long> probes)
Collection<ProcessedExpressionDataVector>	getProcessedDataVectors(ExpressionExperiment expressionExperiment)
Collection<ProcessedExpressionDataVector>	getProcessedDataVectorsAndThaw(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	removeProcessedDataVectors(ExpressionExperiment expressionExperiment)
void	reorderByDesign(ExpressionExperiment ee)	Creates new bioAssayDimensions to match the experimental design, reorders the data to match, updates.
void	replaceProcessedDataVectors(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> vectors)	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	update(Collection<ProcessedExpressionDataVector> updatedVectors)
void	updateRanks(ExpressionExperiment ee)

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

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

Method Detail

replaceProcessedDataVectors

@Secured("GROUP_USER")
void replaceProcessedDataVectors(ExpressionExperiment ee,
                                 Collection<ProcessedExpressionDataVector> vectors)

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

Ranks are recomputed.

Parameters:

ee - ee

vectors - non-persistent, all of the same quantitationtype

updateRanks

@Transactional
@Secured("GROUP_USER")
void updateRanks(ExpressionExperiment ee)

clearCache

@Secured("GROUP_ADMIN")
void clearCache()

createProcessedDataVectors

@Secured("GROUP_USER")
Set<ProcessedExpressionDataVector> createProcessedDataVectors(ExpressionExperiment expressionExperiment)

createProcessedDataVectors

@Secured("GROUP_USER")
Set<ProcessedExpressionDataVector> createProcessedDataVectors(ExpressionExperiment expressionExperiment,
                                                              boolean ignoreInferredScale)
                                                       throws QuantitationMismatchException

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

Throws:

QuantitationMismatchException

getProcessedDataArrays

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

Parameters:

expressionExperiments - - expressionExperiments or expressionExperimentSubSets

genes - genes

Returns:

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

getProcessedDataArrays

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

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

getExpressionLevelsPca

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

Parameters:

expressionExperiment - ee

Returns:

double vector vos

getProcessedDataArrays

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

Retrieves DEDV's by probes and experiments

Parameters:

expressionExperiments - EEs

compositeSequences - composite sequences

Returns:

double vector vos

getProcessedDataArraysByProbeIds

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

getProcessedDataVectors

Collection<ProcessedExpressionDataVector> getProcessedDataVectors(ExpressionExperiment expressionExperiment)

getProcessedDataVectorsAndThaw

Collection<ProcessedExpressionDataVector> getProcessedDataVectorsAndThaw(ExpressionExperiment expressionExperiment)

getRanks

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

getRanks

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

getRanksByProbe

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

getDiffExVectors

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

computeProcessedExpressionData

@Secured("GROUP_ADMIN")
void computeProcessedExpressionData(ExpressionExperiment ee)

Compute processed expression data, ignoring mismatched with the inferred scale.

computeProcessedExpressionData

@Secured("GROUP_ADMIN")
void computeProcessedExpressionData(ExpressionExperiment ee,
                                    boolean ignoreInferredScale)
                             throws QuantitationMismatchException

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

Throws:

QuantitationMismatchException

reorderByDesign

@Secured("GROUP_ADMIN")
void reorderByDesign(ExpressionExperiment ee)

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

Parameters:

eeId - the experiment id

findByExpressionExperiment

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_DATAVECTOR_COLLECTION_READ"})
Collection<ProcessedExpressionDataVector> findByExpressionExperiment(ExpressionExperiment ee,
                                                                     QuantitationType quantitationType)

update

@Secured("GROUP_USER")
void update(Collection<ProcessedExpressionDataVector> updatedVectors)

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.