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

Class DifferentialExpressionAnalysisServiceImpl

java.lang.Object

ubic.gemma.persistence.service.AbstractService<DifferentialExpressionAnalysis>

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

All Implemented Interfaces:

AnalysisService<DifferentialExpressionAnalysis>, DifferentialExpressionAnalysisService, SingleExperimentAnalysisService<DifferentialExpressionAnalysis>, BaseImmutableService<DifferentialExpressionAnalysis>, BaseReadOnlyService<DifferentialExpressionAnalysis>, BaseService<DifferentialExpressionAnalysis>

@Service
public class DifferentialExpressionAnalysisServiceImpl
extends AbstractService<DifferentialExpressionAnalysis>
implements DifferentialExpressionAnalysisService

Author:

paul, keshav

See Also:

DifferentialExpressionAnalysisService

Constructor Summary

Constructors

Constructor	Description
DifferentialExpressionAnalysisServiceImpl(DifferentialExpressionAnalysisDao mainDao)

Method Summary

Modifier and Type	Method	Description
boolean	canDelete(DifferentialExpressionAnalysis differentialExpressionAnalysis)
Integer	countDownregulated(ExpressionAnalysisResultSet par, double threshold)
Integer	countProbesMeetingThreshold(ExpressionAnalysisResultSet ears, double threshold)
Integer	countUpregulated(ExpressionAnalysisResultSet par, double threshold)
Collection<DifferentialExpressionAnalysis>	find(Gene gene, ExpressionAnalysisResultSet resultSet, double threshold)
Collection<DifferentialExpressionAnalysis>	findByExperiment(BioAssaySet experiment)
Map<Long,Collection<DifferentialExpressionAnalysis>>	findByExperimentIds(Collection<Long> experimentIds)
Map<BioAssaySet,Collection<DifferentialExpressionAnalysis>>	findByExperiments(Collection<BioAssaySet> experiments)
Collection<DifferentialExpressionAnalysis>	findByFactor(ExperimentalFactor ef)
Collection<DifferentialExpressionAnalysis>	findByName(String name)
Collection<DifferentialExpressionAnalysis>	findByTaxon(Taxon taxon)
Collection<BioAssaySet>	findExperimentsWithAnalyses(Gene gene)
Map<ExpressionExperiment,Collection<DifferentialExpressionAnalysis>>	getAnalyses(Collection<? extends BioAssaySet> expressionExperiments)
Collection<DifferentialExpressionAnalysis>	getAnalyses(BioAssaySet expressionExperiment)
Map<ExpressionExperimentDetailsValueObject,List<DifferentialExpressionAnalysisValueObject>>	getAnalysesByExperiment(Collection<Long> ids)	Given a set of ids, find experiments or experimentsubsets that have differential expression analyses.
Map<ExpressionExperimentDetailsValueObject,List<DifferentialExpressionAnalysisValueObject>>	getAnalysesByExperiment(Collection<Long> ids, int offset, int limit)
Collection<Long>	getExperimentsWithAnalysis(Collection<Long> idsToFilter)	Not secured: for internal use only
Collection<Long>	getExperimentsWithAnalysis(Taxon taxon)	Not secured: for internal use only
void	remove(Long id)	Removes the entity with given ID from the persistent storage.
void	remove(Collection<DifferentialExpressionAnalysis> entities)	Removes all the given entities from persistent storage.
void	remove(DifferentialExpressionAnalysis toDelete)	Removes the given entity from the persistent storage.
void	removeForExperiment(BioAssaySet ee)	Removes all analyses for the given experiment
int	removeForExperimentalFactor(ExperimentalFactor experimentalFactor)	Remove analyses using the given factor.
int	removeForExperimentalFactors(Collection<ExperimentalFactor> experimentalFactors)
Collection<DifferentialExpressionAnalysis>	thaw(Collection<DifferentialExpressionAnalysis> expressionAnalyses)
DifferentialExpressionAnalysis	thaw(DifferentialExpressionAnalysis differentialExpressionAnalysis)
DifferentialExpressionAnalysis	thawFully(DifferentialExpressionAnalysis differentialExpressionAnalysis)

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

countAll, create, create, ensureInSession, ensureInSession, find, findOrCreate, findOrFail, getElementClass, load, load, loadAll, loadOrFail, loadOrFail, loadOrFail, loadOrFail, 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.analysis.AnalysisService

load, loadAll

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

create, findOrCreate

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

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

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

save, save, update

Methods inherited from interface ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisService

create, update

Constructor Detail

DifferentialExpressionAnalysisServiceImpl

@Autowired
public DifferentialExpressionAnalysisServiceImpl(DifferentialExpressionAnalysisDao mainDao)

Method Detail

countDownregulated

@Transactional(readOnly=true)
public Integer countDownregulated(ExpressionAnalysisResultSet par,
                                  double threshold)

Specified by:

countDownregulated in interface DifferentialExpressionAnalysisService

Parameters:

par - result set

threshold - for corrected pvalue. Results may not be accurate for 'unreasonable' thresholds.

Returns:

number of downregulated elements

countProbesMeetingThreshold

@Transactional(readOnly=true)
public Integer countProbesMeetingThreshold(ExpressionAnalysisResultSet ears,
                                           double threshold)

Specified by:

countProbesMeetingThreshold in interface DifferentialExpressionAnalysisService

Parameters:

ears - result sets

threshold - (double) for corrected pvalue. Results may not be accurate for 'unreasonable' thresholds.

Returns:

an integer count of all the probes that met the given threshold in the given expressionAnalysisResultSet

countUpregulated

@Transactional(readOnly=true)
public Integer countUpregulated(ExpressionAnalysisResultSet par,
                                double threshold)

Specified by:

countUpregulated in interface DifferentialExpressionAnalysisService

Parameters:

par - result set

threshold - for corrected pvalue. Results may not be accurate for 'unreasonable' thresholds.

find

@Transactional(readOnly=true)
public Collection<DifferentialExpressionAnalysis> find(Gene gene,
                                                       ExpressionAnalysisResultSet resultSet,
                                                       double threshold)

Specified by:

find in interface DifferentialExpressionAnalysisService

findByFactor

@Transactional(readOnly=true)
public Collection<DifferentialExpressionAnalysis> findByFactor(ExperimentalFactor ef)

Specified by:

findByFactor in interface DifferentialExpressionAnalysisService

findByExperimentIds

@Transactional(readOnly=true)
public Map<Long,Collection<DifferentialExpressionAnalysis>> findByExperimentIds(Collection<Long> experimentIds)

Specified by:

findByExperimentIds in interface DifferentialExpressionAnalysisService

findByTaxon

@Transactional(readOnly=true)
public Collection<DifferentialExpressionAnalysis> findByTaxon(Taxon taxon)

Specified by:

findByTaxon in interface AnalysisService<DifferentialExpressionAnalysis>

Specified by:

findByTaxon in interface DifferentialExpressionAnalysisService

findExperimentsWithAnalyses

@Transactional(readOnly=true)
public Collection<BioAssaySet> findExperimentsWithAnalyses(Gene gene)

Specified by:

findExperimentsWithAnalyses in interface DifferentialExpressionAnalysisService

getAnalyses

@Transactional(readOnly=true)
public Collection<DifferentialExpressionAnalysis> getAnalyses(BioAssaySet expressionExperiment)

Specified by:

getAnalyses in interface DifferentialExpressionAnalysisService

getAnalyses

@Transactional(readOnly=true)
public Map<ExpressionExperiment,Collection<DifferentialExpressionAnalysis>> getAnalyses(Collection<? extends BioAssaySet> expressionExperiments)

Specified by:

getAnalyses in interface DifferentialExpressionAnalysisService

Parameters:

expressionExperiments - ees

Returns:

quite deeply thawed analyses (not the results themselves, but metadata)

thaw

@Transactional(readOnly=true)
public Collection<DifferentialExpressionAnalysis> thaw(Collection<DifferentialExpressionAnalysis> expressionAnalyses)

Specified by:

thaw in interface DifferentialExpressionAnalysisService

thaw

@Transactional(readOnly=true)
public DifferentialExpressionAnalysis thaw(DifferentialExpressionAnalysis differentialExpressionAnalysis)

Specified by:

thaw in interface DifferentialExpressionAnalysisService

thawFully

@Transactional(readOnly=true)
public DifferentialExpressionAnalysis thawFully(DifferentialExpressionAnalysis differentialExpressionAnalysis)

Specified by:

thawFully in interface DifferentialExpressionAnalysisService

canDelete

@Transactional(readOnly=true)
public boolean canDelete(DifferentialExpressionAnalysis differentialExpressionAnalysis)

Specified by:

canDelete in interface DifferentialExpressionAnalysisService

Parameters:

differentialExpressionAnalysis - analysis

Returns:

Is the analysis deleteable, or is it tied up with another entity that keeps it from being removed.

getAnalysesByExperiment

@Transactional(readOnly=true)
public Map<ExpressionExperimentDetailsValueObject,List<DifferentialExpressionAnalysisValueObject>> getAnalysesByExperiment(Collection<Long> ids)

Description copied from interface: DifferentialExpressionAnalysisService

Given a set of ids, find experiments or experimentsubsets that have differential expression analyses. Subsets are handled two ways: if the ID given is of a subset, or if the ID is of an experiment that has subsets. In the latter case, the return value will contain experiments that were not explicitly queried for.

Specified by:

getAnalysesByExperiment in interface DifferentialExpressionAnalysisService

Parameters:

ids - of experiments or experimentsubsets.

Returns:

map of bioassayset (valueobjects) to analyses (valueobjects) for each.

getAnalysesByExperiment

@Transactional(readOnly=true)
public Map<ExpressionExperimentDetailsValueObject,List<DifferentialExpressionAnalysisValueObject>> getAnalysesByExperiment(Collection<Long> ids,
                                                                                                                                 int offset,
                                                                                                                                 int limit)

Specified by:

getAnalysesByExperiment in interface DifferentialExpressionAnalysisService

remove

@Transactional
public void remove(DifferentialExpressionAnalysis toDelete)

Description copied from interface: BaseImmutableService

Removes the given entity from the persistent storage.

Specified by:

remove in interface AnalysisService<DifferentialExpressionAnalysis>

Specified by:

remove in interface BaseImmutableService<DifferentialExpressionAnalysis>

Overrides:

remove in class AbstractService<DifferentialExpressionAnalysis>

Parameters:

toDelete - the entity to be removed.

remove

public void remove(Collection<DifferentialExpressionAnalysis> entities)

Description copied from interface: BaseImmutableService

Removes all the given entities from persistent storage.

Specified by:

remove in interface BaseImmutableService<DifferentialExpressionAnalysis>

Overrides:

remove in class AbstractService<DifferentialExpressionAnalysis>

Parameters:

entities - the entities to be removed.

remove

public void remove(Long id)

Description copied from interface: BaseImmutableService

Removes the entity with given ID from the persistent storage.

Specified by:

remove in interface BaseImmutableService<DifferentialExpressionAnalysis>

Overrides:

remove in class AbstractService<DifferentialExpressionAnalysis>

Parameters:

id - the ID of entity to be removed.

removeForExperiment

@Transactional
public void removeForExperiment(BioAssaySet ee)

Description copied from interface: SingleExperimentAnalysisService

Removes all analyses for the given experiment

Specified by:

removeForExperiment in interface SingleExperimentAnalysisService<DifferentialExpressionAnalysis>

Parameters:

ee - the expriment to remove all analyses for

removeForExperimentalFactor

@Transactional
public int removeForExperimentalFactor(ExperimentalFactor experimentalFactor)

Description copied from interface: DifferentialExpressionAnalysisService

Remove analyses using the given factor.

Specified by:

removeForExperimentalFactor in interface DifferentialExpressionAnalysisService

Returns:

the number of analysis removed

removeForExperimentalFactors

@Transactional
public int removeForExperimentalFactors(Collection<ExperimentalFactor> experimentalFactors)

Specified by:

removeForExperimentalFactors in interface DifferentialExpressionAnalysisService

findByExperiment

@Transactional(readOnly=true)
public Collection<DifferentialExpressionAnalysis> findByExperiment(BioAssaySet experiment)

Specified by:

findByExperiment in interface SingleExperimentAnalysisService<DifferentialExpressionAnalysis>

Parameters:

experiment - investigation

Returns:

find all the analyses that involved the given investigation

findByExperiments

@Transactional(readOnly=true)
public Map<BioAssaySet,Collection<DifferentialExpressionAnalysis>> findByExperiments(Collection<BioAssaySet> experiments)

Specified by:

findByExperiments in interface SingleExperimentAnalysisService<DifferentialExpressionAnalysis>

Parameters:

experiments - investigations

Returns:

Given a collection of investigations returns a Map of Analysis --> collection of Investigations The collection of investigations returned by the map will include all the investigations for the analysis key iff one of the investigations for that analysis was in the given collection started with

findByName

@Transactional(readOnly=true)
public Collection<DifferentialExpressionAnalysis> findByName(String name)

Specified by:

findByName in interface AnalysisService<DifferentialExpressionAnalysis>

getExperimentsWithAnalysis

@Transactional(readOnly=true)
public Collection<Long> getExperimentsWithAnalysis(Collection<Long> idsToFilter)

Description copied from interface: SingleExperimentAnalysisService

Not secured: for internal use only

Specified by:

getExperimentsWithAnalysis in interface AnalysisService<DifferentialExpressionAnalysis>

Specified by:

getExperimentsWithAnalysis in interface SingleExperimentAnalysisService<DifferentialExpressionAnalysis>

Parameters:

idsToFilter - starting list of bioassayset ids.

Returns:

the ones which have a coexpression analysis.

getExperimentsWithAnalysis

@Transactional(readOnly=true)
public Collection<Long> getExperimentsWithAnalysis(Taxon taxon)

Description copied from interface: SingleExperimentAnalysisService

Not secured: for internal use only

Specified by:

getExperimentsWithAnalysis in interface AnalysisService<DifferentialExpressionAnalysis>

Specified by:

getExperimentsWithAnalysis in interface SingleExperimentAnalysisService<DifferentialExpressionAnalysis>

Parameters:

taxon - taxon

Returns:

ids of bioassaysets from the given taxon that have a coexpression analysis