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

Interface DifferentialExpressionAnalysisService

All Superinterfaces:

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

All Known Implementing Classes:

DifferentialExpressionAnalysisServiceImpl

public interface DifferentialExpressionAnalysisService
extends BaseService<DifferentialExpressionAnalysis>, SingleExperimentAnalysisService<DifferentialExpressionAnalysis>

Author:

kelsey

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)
DifferentialExpressionAnalysis	create(DifferentialExpressionAnalysis analysis)	Creates the given entity in the persistent storage.
Collection<DifferentialExpressionAnalysis>	find(Gene gene, ExpressionAnalysisResultSet resultSet, double threshold)
Map<Long,Collection<DifferentialExpressionAnalysis>>	findByExperimentIds(Collection<Long> investigationIds)
Collection<DifferentialExpressionAnalysis>	findByFactor(ExperimentalFactor ef)
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)
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)
void	update(DifferentialExpressionAnalysis o)	Updates the given entity in the persistent storage.

Methods inherited from interface ubic.gemma.persistence.service.analysis.AnalysisService

findByName, load, loadAll, remove

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

create, findOrCreate, remove, remove

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.SingleExperimentAnalysisService

findByExperiment, findByExperiments, getExperimentsWithAnalysis, getExperimentsWithAnalysis, removeForExperiment

Method Detail

countDownregulated

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Integer countDownregulated(ExpressionAnalysisResultSet par,
                           double threshold)

Parameters:

par - result set

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

Returns:

number of downregulated elements

countProbesMeetingThreshold

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Integer countProbesMeetingThreshold(ExpressionAnalysisResultSet ears,
                                    double threshold)

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

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Integer countUpregulated(ExpressionAnalysisResultSet par,
                         double threshold)

Parameters:

par - result set

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

create

@Secured("GROUP_USER")
DifferentialExpressionAnalysis create(DifferentialExpressionAnalysis analysis)

Description copied from interface: BaseImmutableService

Creates the given entity in the persistent storage.

Specified by:

create in interface BaseImmutableService<DifferentialExpressionAnalysis>

Parameters:

analysis - the entity to be created.

Returns:

object referencing the persistent instance of the given entity.

find

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<DifferentialExpressionAnalysis> find(Gene gene,
                                                ExpressionAnalysisResultSet resultSet,
                                                double threshold)

findByFactor

@Secured("IS_AUTHENTICATED_ANONYMOUSLY")
Collection<DifferentialExpressionAnalysis> findByFactor(ExperimentalFactor ef)

findByExperimentIds

@Secured("IS_AUTHENTICATED_ANONYMOUSLY")
Map<Long,Collection<DifferentialExpressionAnalysis>> findByExperimentIds(Collection<Long> investigationIds)

findByTaxon

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<DifferentialExpressionAnalysis> findByTaxon(Taxon taxon)

Specified by:

findByTaxon in interface AnalysisService<DifferentialExpressionAnalysis>

findExperimentsWithAnalyses

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<BioAssaySet> findExperimentsWithAnalyses(Gene gene)

getAnalyses

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ","AFTER_ACL_COLLECTION_READ"})
Collection<DifferentialExpressionAnalysis> getAnalyses(BioAssaySet expressionExperiment)

getAnalyses

Map<ExpressionExperiment,Collection<DifferentialExpressionAnalysis>> getAnalyses(Collection<? extends BioAssaySet> expressionExperiments)

Parameters:

expressionExperiments - ees

Returns:

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

thaw

@CheckReturnValue
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_COLLECTION_READ"})
Collection<DifferentialExpressionAnalysis> thaw(Collection<DifferentialExpressionAnalysis> expressionAnalyses)

thaw

@CheckReturnValue
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
DifferentialExpressionAnalysis thaw(DifferentialExpressionAnalysis differentialExpressionAnalysis)

thawFully

@CheckReturnValue
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
DifferentialExpressionAnalysis thawFully(DifferentialExpressionAnalysis differentialExpressionAnalysis)

update

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
void update(DifferentialExpressionAnalysis o)

Description copied from interface: BaseService

Updates the given entity in the persistent storage.

Specified by:

update in interface BaseService<DifferentialExpressionAnalysis>

Parameters:

o - the entity to be updated.

canDelete

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
boolean canDelete(DifferentialExpressionAnalysis differentialExpressionAnalysis)

Parameters:

differentialExpressionAnalysis - analysis

Returns:

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

getAnalysesByExperiment

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_VALUE_OBJECT_MAP_READ"})
Map<ExpressionExperimentDetailsValueObject,List<DifferentialExpressionAnalysisValueObject>> getAnalysesByExperiment(Collection<Long> ids)

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.

Parameters:

ids - of experiments or experimentsubsets.

Returns:

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

getAnalysesByExperiment

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_VALUE_OBJECT_MAP_READ"})
Map<ExpressionExperimentDetailsValueObject,List<DifferentialExpressionAnalysisValueObject>> getAnalysesByExperiment(Collection<Long> ids,
                                                                                                                          int offset,
                                                                                                                          int limit)

removeForExperimentalFactor

int removeForExperimentalFactor(ExperimentalFactor experimentalFactor)

Remove analyses using the given factor.

Returns:

the number of analysis removed

removeForExperimentalFactors

int removeForExperimentalFactors(Collection<ExperimentalFactor> experimentalFactors)