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

Interface DifferentialExpressionAnalysisService

All Superinterfaces:

AnalysisService<DifferentialExpressionAnalysis>, BaseImmutableService<DifferentialExpressionAnalysis>, BaseReadOnlyService<DifferentialExpressionAnalysis>, BaseService<DifferentialExpressionAnalysis>, SecurableBaseImmutableService<DifferentialExpressionAnalysis>, SecurableBaseReadOnlyService<DifferentialExpressionAnalysis>, SecurableBaseService<DifferentialExpressionAnalysis>

All Known Implementing Classes:

DifferentialExpressionAnalysisServiceImpl

public interface DifferentialExpressionAnalysisService
extends AnalysisService<DifferentialExpressionAnalysis>, SecurableBaseService<DifferentialExpressionAnalysis>

Service interface for DifferentialExpressionAnalysis.

The methods here have two flavours: by experiments, which is always an ExpressionExperiment and by experiment analyzed which is either a ExpressionExperiment or ExpressionExperimentSubSet.

Author:

kelsey

See Also:

• DifferentialExpressionAnalysisDao

Method Summary

Modifier and Type	Method	Description
boolean	canDelete(DifferentialExpressionAnalysis differentialExpressionAnalysis)
Collection<DifferentialExpressionAnalysis>	findByExperiment(ExpressionExperiment experimentAnalyzed, boolean includeSubSets)
DifferentialExpressionAnalysis	findByExperimentAndAnalysisId(ExpressionExperiment expressionExperiment, boolean includeSubSets, Long analysisId)
Map<ExpressionExperimentDetailsValueObject,Collection<DifferentialExpressionAnalysisValueObject>>	findByExperimentIds(Collection<Long> experimentIds, boolean includeSubSets, boolean includeAssays)	Given a set of ids, find experiments or subsets that have differential expression analyses.
Map<ExpressionExperiment,Collection<DifferentialExpressionAnalysis>>	findByExperiments(Collection<ExpressionExperiment> experiments, boolean includeSubSets)
Collection<DifferentialExpressionAnalysis>	findByFactor(ExperimentalFactor ef)
Collection<DifferentialExpressionAnalysis>	findByName(String name)
Collection<BioAssaySet>	findExperimentsWithAnalyses(Gene gene)
Collection<Long>	getExperimentsWithAnalysis(Collection<Long> experimentIds, boolean includeSubSets)	Obtain IDs of experiments that have analyses.
DifferentialExpressionAnalysis	loadWithExperimentAnalyzed(Long id)
void	removeForExperiment(ExpressionExperiment ee, boolean includeSubSets)	Removes all analyses for the given experiment
int	removeForExperimentalFactor(ExperimentalFactor experimentalFactor)	Remove analyses using the given factor.
int	removeForExperimentalFactors(Collection<ExperimentalFactor> experimentalFactors)
void	removeForExperimentAnalyzed(BioAssaySet experimentAnalyzed)	Remove all analysis for the given experiment or subset.
Collection<DifferentialExpressionAnalysis>	thaw(Collection<DifferentialExpressionAnalysis> expressionAnalyses)
DifferentialExpressionAnalysis	thaw(DifferentialExpressionAnalysis differentialExpressionAnalysis)
DifferentialExpressionAnalysis	thawFully(DifferentialExpressionAnalysis differentialExpressionAnalysis)

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

countAll, getElementClass, loadOrFail, loadOrFail

Methods inherited from interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseImmutableService

create, create, findOrCreate, remove, remove

Methods inherited from interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseReadOnlyService

find, findOrFail, load, load, loadAll, loadOrFail, loadOrFail, loadOrFail, loadOrFail, streamAll, streamAll

Methods inherited from interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseService

save, save, update, update

Method Details

loadWithExperimentAnalyzed

@Nullable
DifferentialExpressionAnalysis loadWithExperimentAnalyzed(Long id)

findByName

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<DifferentialExpressionAnalysis> findByName(String name)

findByFactor

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

findExperimentsWithAnalyses

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

findByExperimentAndAnalysisId

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ","AFTER_ACL_READ"})
DifferentialExpressionAnalysis findByExperimentAndAnalysisId(ExpressionExperiment expressionExperiment,
 boolean includeSubSets,
 Long analysisId)

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)

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.

findByExperimentIds

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_VALUE_OBJECT_MAP_READ"})
Map<ExpressionExperimentDetailsValueObject,Collection<DifferentialExpressionAnalysisValueObject>> findByExperimentIds(Collection<Long> experimentIds,
 boolean includeSubSets,
 boolean includeAssays)

Given a set of ids, find experiments or subsets 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:

experimentIds - of ExpressionExperiment

includeSubSets - include analysis of subsets of the requested experiments

includeAssays - include assay information in the value objects

Returns:

map of detailed EE VOs to analyses VOs for each, subset analyses are mapped to their source experiment

removeForExperimentalFactor

int removeForExperimentalFactor(ExperimentalFactor experimentalFactor)

Remove analyses using the given factor.

Returns:

the number of analysis removed

removeForExperimentalFactors

int removeForExperimentalFactors(Collection<ExperimentalFactor> experimentalFactors)

findByExperiment

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COLLECTION_READ"})
Collection<DifferentialExpressionAnalysis> findByExperiment(ExpressionExperiment experimentAnalyzed,
 boolean includeSubSets)

Parameters:

experimentAnalyzed - experiment analyzed

includeSubSets - include analyses for its ExpressionExperimentSubSet

Returns:

find all the analyses that involved the given investigation

findByExperiments

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_COLLECTION_READ","AFTER_ACL_MAP_READ"})
Map<ExpressionExperiment,Collection<DifferentialExpressionAnalysis>> findByExperiments(Collection<ExpressionExperiment> experiments,
 boolean includeSubSets)

Parameters:

experiments - investigations

includeSubSets - include analyses for their ExpressionExperimentSubSet

Returns:

analyses grouped by experiment, subset analyses are mapped to their source experiment

getExperimentsWithAnalysis

Collection<Long> getExperimentsWithAnalysis(Collection<Long> experimentIds,
 boolean includeSubSets)

Obtain IDs of experiments that have analyses.

Not secured: for internal use only

Parameters:

experimentIds - starting list of ExpressionExperiment IDs

includeSubSets - include IDs of their subsets that have analyses

Returns:

the ones which have an analysis

removeForExperiment

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
void removeForExperiment(ExpressionExperiment ee,
 boolean includeSubSets)

Removes all analyses for the given experiment

Parameters:

ee - the expriment to remove all analyses for

includeSubSets - also delete analyses of its ExpressionExperimentSubSet.

removeForExperimentAnalyzed

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
void removeForExperimentAnalyzed(BioAssaySet experimentAnalyzed)

Remove all analysis for the given experiment or subset.