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

Class DifferentialExpressionResultServiceImpl

java.lang.Object

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

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

All Implemented Interfaces:

DifferentialExpressionResultService, BaseImmutableService<DifferentialExpressionAnalysisResult>, BaseReadOnlyService<DifferentialExpressionAnalysisResult>, BaseService<DifferentialExpressionAnalysisResult>

@Service
public class DifferentialExpressionResultServiceImpl
extends AbstractService<DifferentialExpressionAnalysisResult>
implements DifferentialExpressionResultService

Author:

keshav

See Also:

• DifferentialExpressionResultService

Field Summary

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

log

Constructor Summary

Constructors

Constructor	Description
DifferentialExpressionResultServiceImpl(DifferentialExpressionResultDao DERDao)

Method Summary

Modifier and Type	Method	Description
Map<BioAssaySetValueObject,List<DifferentialExpressionValueObject>>	findByExperimentAnalyzed(Collection<? extends BioAssaySet> experimentsAnalyzed, boolean includeSubSets, double threshold, 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<BioAssaySetValueObject,List<DifferentialExpressionValueObject>>	findByGene(Gene gene, boolean keepNonSpecificProbes)	Returns a map of a collection of DifferentialExpressionAnalysisResults keyed by ExpressionExperiment.
Map<BioAssaySetValueObject,List<DifferentialExpressionValueObject>>	findByGene(Gene gene, boolean keepNonSpecificProbes, double threshold, int limit)	Find differential expression for a gene, exceeding a given significance level (using the corrected pvalue field)
Map<BioAssaySetValueObject,List<DifferentialExpressionValueObject>>	findByGeneAndExperimentAnalyzed(Gene gene, boolean keepNonSpecificProbes, Collection<? extends BioAssaySet> experimentsAnalyzed, boolean includeSubSets)	Returns a map of a collection of DifferentialExpressionAnalysisResults keyed by ExpressionExperiment.
Map<BioAssaySetValueObject,List<DifferentialExpressionValueObject>>	findByGeneAndExperimentAnalyzed(Gene gene, boolean keepNonSpecificProbes, Collection<? extends BioAssaySet> experimentsAnalyzed, boolean includeSubSets, double threshold, int limit)	Find differential expression for a gene in given data sets, exceeding a given significance level (using the corrected pvalue field)
List<DifferentialExpressionAnalysisResult>	findByGeneAndExperimentAnalyzedIds(Gene gene, boolean keepNonSpecific, Collection<Long> experimentAnalyzedIds, boolean includeSubSets, Map<DifferentialExpressionAnalysisResult,Long> sourceExperimentIdMap, Map<DifferentialExpressionAnalysisResult,Long> experimentAnalyzedIdMap, Map<DifferentialExpressionAnalysisResult,Baseline> baselineMap, double threshold, boolean initializeFactorValues)
Map<Long,Map<Long,DiffExprGeneSearchResult>>	findDiffExAnalysisResultIdsInResultSets(Collection<DiffExResultSetSummaryValueObject> resultSets, Collection<Long> geneIds)	Retrieve differential expression results in bulk.
List<DifferentialExpressionValueObject>	findInResultSet(ExpressionAnalysisResultSet resultSet, Double threshold, int maxResultsToReturn, int minNumberOfResults)
Map<Long,ContrastsValueObject>	loadContrastDetailsForResults(Collection<Long> ids)

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, remove, remove, remove, save, save, streamAll, streamAll, 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.BaseReadOnlyService

countAll, find, findOrFail, getElementClass, load, load, loadAll, loadOrFail, loadOrFail, loadOrFail, loadOrFail, streamAll, streamAll

Constructor Details

DifferentialExpressionResultServiceImpl

@Autowired
public DifferentialExpressionResultServiceImpl(DifferentialExpressionResultDao DERDao)

Method Details

findByGeneAndExperimentAnalyzedIds

@Transactional(readOnly=true)
public List<DifferentialExpressionAnalysisResult> findByGeneAndExperimentAnalyzedIds(Gene gene,
 boolean keepNonSpecific,
 Collection<Long> experimentAnalyzedIds,
 boolean includeSubSets,
 Map<DifferentialExpressionAnalysisResult,Long> sourceExperimentIdMap,
 Map<DifferentialExpressionAnalysisResult,Long> experimentAnalyzedIdMap,
 Map<DifferentialExpressionAnalysisResult,Baseline> baselineMap,
 double threshold,
 boolean initializeFactorValues)

Specified by:

findByGeneAndExperimentAnalyzedIds in interface DifferentialExpressionResultService

See Also:

• DifferentialExpressionResultDao.findByGeneAndExperimentAnalyzed(Gene, Collection, boolean, Map, Map, Map, double, boolean, boolean)

findByExperimentAnalyzed

@Transactional(readOnly=true)
public Map<BioAssaySetValueObject,List<DifferentialExpressionValueObject>> findByExperimentAnalyzed(Collection<? extends BioAssaySet> experimentsAnalyzed,
 boolean includeSubSets,
 double threshold,
 int limit)

Description copied from interface: DifferentialExpressionResultService

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 DifferentialExpressionResultService

Parameters:

experimentsAnalyzed - ees

includeSubSets - if true, include the subsets of the experiments analyzed

threshold - threshold

limit - limit

Returns:

map to diff ex VOs

findByGene

@Transactional(readOnly=true)
public Map<BioAssaySetValueObject,List<DifferentialExpressionValueObject>> findByGene(Gene gene,
 boolean keepNonSpecificProbes)

Description copied from interface: DifferentialExpressionResultService

Returns a map of a collection of DifferentialExpressionAnalysisResults keyed by ExpressionExperiment.

Specified by:

findByGene in interface DifferentialExpressionResultService

Parameters:

gene - gene

keepNonSpecificProbes -

Returns:

map to diff ex VOs

findByGene

@Transactional(readOnly=true)
public Map<BioAssaySetValueObject,List<DifferentialExpressionValueObject>> findByGene(Gene gene,
 boolean keepNonSpecificProbes,
 double threshold,
 int limit)

Description copied from interface: DifferentialExpressionResultService

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

Specified by:

findByGene in interface DifferentialExpressionResultService

Parameters:

gene - gene

keepNonSpecificProbes -

threshold - threshold

limit - limit

Returns:

map to diff ex VOs

findByGeneAndExperimentAnalyzed

@Transactional(readOnly=true)
public Map<BioAssaySetValueObject,List<DifferentialExpressionValueObject>> findByGeneAndExperimentAnalyzed(Gene gene,
 boolean keepNonSpecificProbes,
 Collection<? extends BioAssaySet> experimentsAnalyzed,
 boolean includeSubSets)

Description copied from interface: DifferentialExpressionResultService

Returns a map of a collection of DifferentialExpressionAnalysisResults keyed by ExpressionExperiment.

Specified by:

findByGeneAndExperimentAnalyzed in interface DifferentialExpressionResultService

Parameters:

gene - gene

keepNonSpecificProbes -

experimentsAnalyzed - ees

includeSubSets -

Returns:

map to diff ex VOs

findByGeneAndExperimentAnalyzed

@Transactional(readOnly=true)
public Map<BioAssaySetValueObject,List<DifferentialExpressionValueObject>> findByGeneAndExperimentAnalyzed(Gene gene,
 boolean keepNonSpecificProbes,
 Collection<? extends BioAssaySet> experimentsAnalyzed,
 boolean includeSubSets,
 double threshold,
 int limit)

Description copied from interface: DifferentialExpressionResultService

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 DifferentialExpressionResultService

Parameters:

gene - gene

keepNonSpecificProbes -

experimentsAnalyzed - ees

includeSubSets -

threshold - threshold

limit - limit

Returns:

map to diff ex VOs

findDiffExAnalysisResultIdsInResultSets

@Transactional(readOnly=true)
public Map<Long,Map<Long,DiffExprGeneSearchResult>> findDiffExAnalysisResultIdsInResultSets(Collection<DiffExResultSetSummaryValueObject> resultSets,
 Collection<Long> geneIds)

Description copied from interface: DifferentialExpressionResultService

Retrieve differential expression results in bulk. This is an important method for the differential expression interfaces.

Specified by:

findDiffExAnalysisResultIdsInResultSets in interface DifferentialExpressionResultService

Parameters:

resultSets - result sets

geneIds - gene ids

Returns:

map of resultset IDs to map of gene id to differential expression results.

findInResultSet

@Transactional(readOnly=true)
public List<DifferentialExpressionValueObject> findInResultSet(ExpressionAnalysisResultSet resultSet,
 Double threshold,
 int maxResultsToReturn,
 int minNumberOfResults)

Specified by:

findInResultSet in interface DifferentialExpressionResultService

loadContrastDetailsForResults

@Transactional(readOnly=true)
public Map<Long,ContrastsValueObject> loadContrastDetailsForResults(Collection<Long> ids)

Specified by:

loadContrastDetailsForResults in interface DifferentialExpressionResultService

Parameters:

ids - ids

Returns:

map of result to contrasts value object.