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

Interface ProcessedExpressionDataVectorDao

All Superinterfaces:

BaseDao<ProcessedExpressionDataVector>, DesignElementDataVectorDao<ProcessedExpressionDataVector>

All Known Implementing Classes:

ProcessedExpressionDataVectorDaoImpl

public interface ProcessedExpressionDataVectorDao
extends DesignElementDataVectorDao<ProcessedExpressionDataVector>

Author:

Paul

Nested Class Summary

Nested Classes

Modifier and Type	Interface	Description
static class	ProcessedExpressionDataVectorDao.RankMethod

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 expressionExperiment)
List<ProcessedExpressionDataVector>	getProcessedVectors(ExpressionExperiment expressionExperiment, 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)
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 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

Method Detail

createProcessedDataVectors

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

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).

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

Collection<ProcessedExpressionDataVector> getProcessedVectors(ExpressionExperiment expressionExperiment)

Parameters:

expressionExperiment - ee

Returns:

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

getProcessedVectors

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

Retrieve a slice of processed vectors.

getProcessedVectorsAndGenes

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

Obtain processed expression vectors with their associated genes.

Parameters:

cs2gene - Map of probe to genes.

ees - ees

Returns:

map of vectors to genes.

getRandomProcessedVectors

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

getProcessedVectorsDesignElements

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

Only retrieve the design elements for a slice of vectors.

getRanks

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

getRanks

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

getGenes

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

Obtain the genes associated to each vector.