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<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>>	find(Collection<Long> experimentsAnalyzed, 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<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>>	find(Gene gene)	Returns a map of a collection of DifferentialExpressionAnalysisResults keyed by ExpressionExperiment.
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>>	find(Gene gene, Collection<Long> experimentsAnalyzed)	Returns a map of a collection of DifferentialExpressionAnalysisResults keyed by ExpressionExperiment.
Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>>	find(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)
List<DifferentialExpressionAnalysisResult>	findByGeneAndExperimentAnalyzed(Gene gene, Collection<Long> experimentAnalyzedIds, Map<DifferentialExpressionAnalysisResult,Long> sourceExperimentIdMap, Map<DifferentialExpressionAnalysisResult,Long> experimentAnalyzedIdMap, Map<DifferentialExpressionAnalysisResult,Baseline> baselineMap, double threshold, boolean keepNonSpecific, 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, 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

Constructor Detail

DifferentialExpressionResultServiceImpl

@Autowired
public DifferentialExpressionResultServiceImpl(DifferentialExpressionResultDao DERDao)

Method Detail

findByGeneAndExperimentAnalyzed

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

Specified by:

findByGeneAndExperimentAnalyzed in interface DifferentialExpressionResultService

See Also:

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

find

@Transactional(readOnly=true)
public Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>> find(Collection<Long> experimentsAnalyzed,
                                                                                               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:

find in interface DifferentialExpressionResultService

Parameters:

experimentsAnalyzed - ees

threshold - threshold

limit - limit

Returns:

map to diff ex VOs

find

@Transactional(readOnly=true)
public Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>> find(Gene gene)

Description copied from interface: DifferentialExpressionResultService

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

Specified by:

find in interface DifferentialExpressionResultService

Parameters:

gene - gene

Returns:

map to diff ex VOs

find

@Transactional(readOnly=true)
public Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>> find(Gene gene,
                                                                                               Collection<Long> experimentsAnalyzed)

Description copied from interface: DifferentialExpressionResultService

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

Specified by:

find in interface DifferentialExpressionResultService

Parameters:

gene - gene

experimentsAnalyzed - ees

Returns:

map to diff ex VOs

find

@Transactional(readOnly=true)
public Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>> find(Gene gene,
                                                                                               Collection<Long> experimentsAnalyzed,
                                                                                               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:

find in interface DifferentialExpressionResultService

Parameters:

gene - gene

experimentsAnalyzed - ees

threshold - threshold

limit - limit

Returns:

map to diff ex VOs

find

@Transactional(readOnly=true)
public Map<ExpressionExperimentValueObject,List<DifferentialExpressionValueObject>> find(Gene gene,
                                                                                               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:

find in interface DifferentialExpressionResultService

Parameters:

gene - gene

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.