Package ubic.gemma.persistence.service.analysis.expression.diff

Class DifferentialExpressionResultDaoImpl

java.lang.Object

ubic.gemma.persistence.service.AbstractDao<DifferentialExpressionAnalysisResult>

ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultDaoImpl

All Implemented Interfaces:

DifferentialExpressionResultDao, BaseDao<DifferentialExpressionAnalysisResult>

@Repository
public class DifferentialExpressionResultDaoImpl
extends AbstractDao<DifferentialExpressionAnalysisResult>
implements DifferentialExpressionResultDao

This is a key class for queries to retrieve differential expression results (as well as standard CRUD aspects of working with DifferentialExpressionResults).

Author:

keshav

Field Summary

Fields inherited from class ubic.gemma.persistence.service.AbstractDao

elementClass, log

Constructor Summary

Constructors

Constructor	Description
DifferentialExpressionResultDaoImpl(SessionFactory sessionFactory, DifferentialExpressionResultCache differentialExpressionResultCache)

Method Summary

Modifier and Type	Method	Description
Collection<DifferentialExpressionAnalysisResult>	create(Collection<DifferentialExpressionAnalysisResult> entities)	Crates all the given entities in the persistent storage.
Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>>	find(Gene gene, double threshold, int limit)	Find differential expression for a gene, exceeding a given significance level (using the corrected pvalue field)
Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>>	findByExperimentAnalyzed(Collection<Long> experiments, double qvalueThreshold, int limit)	Given a list of experiments and a threshold value finds all the probes that met the cut off in the given experiments
Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>>	findByGene(Gene gene)	Find differential expression results for a given gene, grouped by experiment.
Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>>	findByGeneAndExperimentAnalyzed(Gene gene, Collection<Long> experimentsAnalyzed)	Find differential expression results for a given gene and set of experiments, grouped by experiment.
Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>>	findByGeneAndExperimentAnalyzed(Gene gene, Collection<Long> experimentsAnalyzed, double threshold, int limit)	Find differential expression for a gene in given data sets, exceeding a given significance level (using the corrected pvalue field)
Map<Long,Map<Long,DiffExprGeneSearchResult>>	findDiffExAnalysisResultIdsInResultSets(Collection<DiffExResultSetSummaryValueObject> resultSets, Collection<Long> geneIds)
List<DifferentialExpressionValueObject>	findInResultSet(ExpressionAnalysisResultSet resultSet, Double threshold, int limit, int minNumberOfResults)
Collection<DifferentialExpressionAnalysisResult>	loadAll()	Loads all instanced of specific class from the persistent storage.
Map<Long,ContrastsValueObject>	loadContrastDetailsForResults(Collection<Long> ids)	Key method for getting contrasts associated with results.
Histogram	loadPvalueDistribution(Long resultSetId)
void	remove(DifferentialExpressionAnalysisResult entity)	Remove a persistent instance

Methods inherited from class ubic.gemma.persistence.service.AbstractDao

countAll, create, find, findByProperty, findByPropertyIn, findOneByProperty, findOrCreate, getBatchSize, getElementClass, getIdentifierPropertyName, getSessionFactory, load, load, loadReference, loadReference, remove, remove, save, save, 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, find, findOrCreate, getElementClass, getIdentifierPropertyName, load, load, loadReference, loadReference, remove, remove, save, save, update, update

Constructor Detail

DifferentialExpressionResultDaoImpl

@Autowired
public DifferentialExpressionResultDaoImpl(SessionFactory sessionFactory,
                                           DifferentialExpressionResultCache differentialExpressionResultCache)

Method Detail

create

public Collection<DifferentialExpressionAnalysisResult> create(Collection<DifferentialExpressionAnalysisResult> entities)

Description copied from interface: BaseDao

Crates all the given entities in the persistent storage.

Specified by:

create in interface BaseDao<DifferentialExpressionAnalysisResult>

Overrides:

create in class AbstractDao<DifferentialExpressionAnalysisResult>

Parameters:

entities - the entities to be crated.

Returns:

collection of entities representing the instances in the persistent storage that were created.

remove

public void remove(DifferentialExpressionAnalysisResult entity)

Description copied from interface: BaseDao

Remove a persistent instance

Specified by:

remove in interface BaseDao<DifferentialExpressionAnalysisResult>

Overrides:

remove in class AbstractDao<DifferentialExpressionAnalysisResult>

Parameters:

entity - the entity to be removed

findByGeneAndExperimentAnalyzed

public Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>> findByGeneAndExperimentAnalyzed(Gene gene,
                                                                                                                          Collection<Long> experimentsAnalyzed,
                                                                                                                          double threshold,
                                                                                                                          int limit)

Description copied from interface: DifferentialExpressionResultDao

Find differential expression for a gene in given data sets, exceeding a given significance level (using the corrected pvalue field)

Specified by:

findByGeneAndExperimentAnalyzed in interface DifferentialExpressionResultDao

findByExperimentAnalyzed

public Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>> findByExperimentAnalyzed(Collection<Long> experiments,
                                                                                                                   double qvalueThreshold,
                                                                                                                   int limit)

Description copied from interface: DifferentialExpressionResultDao

Given a list of experiments and a threshold value finds all the probes that met the cut off in the given experiments

Specified by:

findByExperimentAnalyzed in interface DifferentialExpressionResultDao

findByGene

public Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>> findByGene(Gene gene)

Description copied from interface: DifferentialExpressionResultDao

Find differential expression results for a given gene, grouped by experiment.

Specified by:

findByGene in interface DifferentialExpressionResultDao

Returns:

a map of a collection of DifferentialExpressionAnalysisResults keyed by BioAssaySet.

findByGeneAndExperimentAnalyzed

public Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>> findByGeneAndExperimentAnalyzed(Gene gene,
                                                                                                                          Collection<Long> experimentsAnalyzed)

Description copied from interface: DifferentialExpressionResultDao

Find differential expression results for a given gene and set of experiments, grouped by experiment.

Specified by:

findByGeneAndExperimentAnalyzed in interface DifferentialExpressionResultDao

Returns:

a map of a collection of DifferentialExpressionAnalysisResults keyed by BioAssaySet.

findDiffExAnalysisResultIdsInResultSets

public Map<Long,Map<Long,DiffExprGeneSearchResult>> findDiffExAnalysisResultIdsInResultSets(Collection<DiffExResultSetSummaryValueObject> resultSets,
                                                                                                        Collection<Long> geneIds)

Specified by:

findDiffExAnalysisResultIdsInResultSets in interface DifferentialExpressionResultDao

Returns:

map of resultSetId to map of gene to DiffExprGeneSearchResult

findInResultSet

public List<DifferentialExpressionValueObject> findInResultSet(ExpressionAnalysisResultSet resultSet,
                                                               Double threshold,
                                                               int limit,
                                                               int minNumberOfResults)

Specified by:

findInResultSet in interface DifferentialExpressionResultDao

loadContrastDetailsForResults

public Map<Long,ContrastsValueObject> loadContrastDetailsForResults(Collection<Long> ids)

Key method for getting contrasts associated with results.

Specified by:

loadContrastDetailsForResults in interface DifferentialExpressionResultDao

find

public Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>> find(Gene gene,
                                                                                               double threshold,
                                                                                               int limit)

Description copied from interface: DifferentialExpressionResultDao

Find differential expression for a gene, exceeding a given significance level (using the corrected pvalue field)

Specified by:

find in interface DifferentialExpressionResultDao

Parameters:

gene - gene

threshold - threshold

limit - limit

Returns:

map to diff exp VOs

loadPvalueDistribution

public Histogram loadPvalueDistribution(Long resultSetId)

Specified by:

loadPvalueDistribution in interface DifferentialExpressionResultDao

loadAll

public Collection<DifferentialExpressionAnalysisResult> loadAll()

Description copied from interface: BaseDao

Loads all instanced of specific class from the persistent storage.

Specified by:

loadAll in interface BaseDao<DifferentialExpressionAnalysisResult>

Overrides:

loadAll in class AbstractDao<DifferentialExpressionAnalysisResult>

Returns:

a collection containing all instances that are currently accessible.