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

log

Constructor Summary

Constructors

Constructor	Description
ProcessedExpressionDataVectorDaoImpl(SessionFactory sessionFactory)

Method Summary

Modifier and Type	Method	Description
int	createProcessedDataVectors(ExpressionExperiment expressionExperiment, boolean ignoreQuantitationMismatch)	Populate the processed data for the given experiment.
Map<ProcessedExpressionDataVector,Collection<Long>>	getGenes(Collection<ProcessedExpressionDataVector> vectors)	Obtain the genes associated to each vector.
Collection<ProcessedExpressionDataVector>	getProcessedVectors(ExpressionExperiment ee)
List<ProcessedExpressionDataVector>	getProcessedVectors(ExpressionExperiment ee, BioAssayDimension dimension, int offset, int limit)	Retrieve a slice of processed vectors.
Map<ProcessedExpressionDataVector,Collection<Long>>	getProcessedVectorsAndGenes(Collection<ExpressionExperiment> ees, Map<Long,Collection<Long>> cs2gene)	Obtain processed expression vectors with their associated genes.
List<CompositeSequence>	getProcessedVectorsDesignElements(ExpressionExperiment ee, BioAssayDimension dimension, int offset, int limit)	Only retrieve the design elements for a slice of vectors.
Collection<ProcessedExpressionDataVector>	getRandomProcessedVectors(ExpressionExperiment ee, int limit)	Obtain a random sample of processed vectors for the given experiment.
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)

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, reload, reload, remove, remove, remove, save, save, streamAll, streamAll, streamQuery, 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, reload, reload, remove, remove, remove, save, save, streamAll, streamAll, 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)

Method Detail

createProcessedDataVectors

public int createProcessedDataVectors(ExpressionExperiment expressionExperiment,
                                      boolean ignoreQuantitationMismatch)
                               throws QuantitationTypeDetectionException,
                                      QuantitationTypeConversionException

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:

expressionExperiment - 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 number of created vectors

Throws:

QuantitationTypeDetectionException

QuantitationTypeConversionException

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.

getProcessedVectors

public List<ProcessedExpressionDataVector> getProcessedVectors(ExpressionExperiment ee,
                                                               BioAssayDimension dimension,
                                                               int offset,
                                                               int limit)

Description copied from interface: ProcessedExpressionDataVectorDao

Retrieve a slice of processed vectors.

Specified by:

getProcessedVectors in interface ProcessedExpressionDataVectorDao

getProcessedVectorsAndGenes

public Map<ProcessedExpressionDataVector,Collection<Long>> getProcessedVectorsAndGenes(@Nullable
                                                                                             Collection<ExpressionExperiment> ees,
                                                                                             Map<Long,Collection<Long>> cs2gene)

Description copied from interface: ProcessedExpressionDataVectorDao

Obtain processed expression vectors with their associated genes.

Specified by:

getProcessedVectorsAndGenes in interface ProcessedExpressionDataVectorDao

Parameters:

ees - ees

cs2gene - Map of probe to genes.

Returns:

map of vectors to genes.

getRandomProcessedVectors

public Collection<ProcessedExpressionDataVector> getRandomProcessedVectors(ExpressionExperiment ee,
                                                                           int limit)

Obtain a random sample of processed vectors for the given experiment.

Specified by:

getRandomProcessedVectors in interface ProcessedExpressionDataVectorDao

Parameters:

ee - ee

limit - if >0, you will get a "random" set of vectors for the experiment

Returns:

processed data vectors

getProcessedVectorsDesignElements

public List<CompositeSequence> getProcessedVectorsDesignElements(ExpressionExperiment ee,
                                                                 BioAssayDimension dimension,
                                                                 int offset,
                                                                 int limit)

Description copied from interface: ProcessedExpressionDataVectorDao

Only retrieve the design elements for a slice of vectors.

Specified by:

getProcessedVectorsDesignElements in interface ProcessedExpressionDataVectorDao

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

getGenes

public Map<ProcessedExpressionDataVector,Collection<Long>> getGenes(Collection<ProcessedExpressionDataVector> vectors)

Description copied from interface: ProcessedExpressionDataVectorDao

Obtain the genes associated to each vector.

Specified by:

getGenes in interface ProcessedExpressionDataVectorDao