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 enum	ProcessedExpressionDataVectorDao.RankMethod

Method Summary

Modifier and Type	Method	Description
Collection<ProcessedExpressionDataVector>	find(Collection<CompositeSequence> designElements, QuantitationType quantitationType)	Retrieve the processed vectors for a set of design elements within a given quantitation type.
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 BaseDao

countAll, create, create, find, findOrCreate, getElementClass, load, load, loadAll, loadReference, loadReference, reload, reload, remove, remove, save, save, streamAll, streamAll, update, update

Methods inherited from interface DesignElementDataVectorDao

find, find, find, findByExpressionExperiment, thaw, thaw

Method Details

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:

ees - ees

cs2gene - Map of probe to genes.

Returns:

map of vectors to genes.

find

Collection<ProcessedExpressionDataVector> find(Collection<CompositeSequence> designElements,
 QuantitationType quantitationType)

Retrieve the processed vectors for a set of design elements within a given quantitation type. Symmetric with RawExpressionDataVectorDao.find(Collection, QuantitationType). Returns the stored entities, whose data has NOT had read-time outlier masking applied — used to recover un-masked values for a previously selected set of probes.

Parameters:

designElements - probes to retrieve; empty collection yields an empty result.

quantitationType - the (processed) quantitation type; scopes the result to a single experiment.

Returns:

the matching processed vectors, thawed for the bioAssayDimension / quantitationType / designElement.

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.