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

Class DifferentialExpressionResultDaoImpl

java.lang.Object

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

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

All Implemented Interfaces:

DifferentialExpressionResultDao, BaseDao<DifferentialExpressionAnalysisResult>

@Repository
public class DifferentialExpressionResultDaoImpl
extends AbstractDao<DifferentialExpressionAnalysisResult>
implements DifferentialExpressionResultDao

This is a key class for queries to retrieve differential expression results (as well as standard CRUD aspects of working with DifferentialExpressionResults).

Author:

keshav

Field Summary

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

log

Constructor Summary

Constructors

Constructor	Description
DifferentialExpressionResultDaoImpl(SessionFactory sessionFactory, DifferentialExpressionResultCache differentialExpressionResultCache)

Method Summary

Modifier and Type	Method	Description
Collection<DifferentialExpressionAnalysisResult>	create(Collection<DifferentialExpressionAnalysisResult> entities)	Create all the given entities in the persistent storage.
Map<BioAssaySet,List<DifferentialExpressionAnalysisResult>>	findByExperimentAnalyzed(Collection<Long> experimentAnalyzedIds, 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<BioAssaySet,List<DifferentialExpressionAnalysisResult>>	findByGene(Gene gene, boolean useGene2Cs, boolean keepNonSpecificProbes)	Find differential expression results for a given gene, grouped by experiment.
Map<BioAssaySet,List<DifferentialExpressionAnalysisResult>>	findByGene(Gene gene, boolean useGene2Cs, boolean keepNonSpecificProbes, double threshold, int limit)	Find differential expression for a gene, exceeding a given significance level (using the corrected pvalue field)
Map<BioAssaySet,List<DifferentialExpressionAnalysisResult>>	findByGeneAndExperimentAnalyzed(Gene gene, boolean useGene2Cs, boolean keepNonSpecificProbes, Collection<Long> experimentAnalyzedIds, boolean includeSubSets)	Find differential expression results for a given gene and set of experiments, grouped by experiment.
Map<BioAssaySet,List<DifferentialExpressionAnalysisResult>>	findByGeneAndExperimentAnalyzed(Gene gene, boolean useGene2Cs, boolean keepNonSpecificProbes, Collection<Long> experimentAnalyzedIds, 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>	findByGeneAndExperimentAnalyzed(Gene gene, Collection<Long> experimentAnalyzedIds, boolean includeSubsets, Map<DifferentialExpressionAnalysisResult,Long> sourceExperimentIdMap, Map<DifferentialExpressionAnalysisResult,Long> experimentAnalyzedIdMap, Map<DifferentialExpressionAnalysisResult,Baseline> baselineMap, double threshold, boolean useGene2Cs, boolean keepNonSpecificProbes, boolean initializeFactorValues)	Retrieve differential expression results for a given gene across all the given datasets.
List<DifferentialExpressionValueObject>	findByResultSet(ExpressionAnalysisResultSet resultSet, double threshold, int limit, int minNumberOfResults)
Map<Long,ContrastsValueObject>	findContrastsByAnalysisResultIds(Collection<Long> ids)	Key method for getting contrasts associated with results.
Map<Long,Map<Long,DiffExprGeneSearchResult>>	findGeneResultsByResultSetIdsAndGeneIds(Collection<DiffExResultSetSummaryValueObject> resultSets, Collection<Long> geneIds)	Retrieve differential expression results in bulk.
Collection<DifferentialExpressionAnalysisResult>	loadAll()	Loads all entities of type BaseDao from the persistent storage.
void	remove(DifferentialExpressionAnalysisResult entity)	Remove a persistent entity.

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

countAll, create, find, findByProperty, findByPropertyIn, findIdByProperty, findOneByProperty, findOrCreate, getBatchSize, getElementClass, getEntityName, getIdentifierPropertyName, getSessionFactory, load, load, loadReference, loadReference, reload, reload, remove, save, save, streamAll, streamAll, streamQuery, 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.BaseDao

countAll, create, find, findOrCreate, getElementClass, load, load, loadReference, loadReference, reload, reload, remove, save, save, streamAll, streamAll, update, update

Constructor Details

DifferentialExpressionResultDaoImpl

@Autowired
public DifferentialExpressionResultDaoImpl(SessionFactory sessionFactory,
 DifferentialExpressionResultCache differentialExpressionResultCache)

Method Details

loadAll

public Collection<DifferentialExpressionAnalysisResult> loadAll()

Description copied from interface: BaseDao

Loads all entities of type BaseDao from the persistent storage.

Specified by:

loadAll in interface BaseDao<DifferentialExpressionAnalysisResult>

Overrides:

loadAll in class AbstractDao<DifferentialExpressionAnalysisResult>

Returns:

a collection containing all entities that are currently accessible.

create

public Collection<DifferentialExpressionAnalysisResult> create(Collection<DifferentialExpressionAnalysisResult> entities)

Description copied from interface: BaseDao

Create all the given entities in the persistent storage.

Specified by:

create in interface BaseDao<DifferentialExpressionAnalysisResult>

Overrides:

create in class AbstractDao<DifferentialExpressionAnalysisResult>

Parameters:

entities - the entities to be crated.

Returns:

collection of entities representing the entities in the persistent storage that were created.

remove

public void remove(DifferentialExpressionAnalysisResult entity)

Description copied from interface: BaseDao

Remove a persistent entity.

Specified by:

remove in interface BaseDao<DifferentialExpressionAnalysisResult>

Overrides:

remove in class AbstractDao<DifferentialExpressionAnalysisResult>

Parameters:

entity - the entity to be removed

findByGeneAndExperimentAnalyzed

public List<DifferentialExpressionAnalysisResult> findByGeneAndExperimentAnalyzed(Gene gene,
 Collection<Long> experimentAnalyzedIds,
 boolean includeSubsets,
 @Nullable
 Map<DifferentialExpressionAnalysisResult,Long> sourceExperimentIdMap,
 @Nullable
 Map<DifferentialExpressionAnalysisResult,Long> experimentAnalyzedIdMap,
 @Nullable
 Map<DifferentialExpressionAnalysisResult,Baseline> baselineMap,
 double threshold,
 boolean useGene2Cs,
 boolean keepNonSpecificProbes,
 boolean initializeFactorValues)

Description copied from interface: DifferentialExpressionResultDao

Retrieve differential expression results for a given gene across all the given datasets.

Results are grouped by result set. If a gene maps to more than one probe, the result with the lowest corrected P-value is selected.

Specified by:

findByGeneAndExperimentAnalyzed in interface DifferentialExpressionResultDao

Parameters:

gene - a specific gene to retrieve differential expression for

experimentAnalyzedIds - list of IDs of experiments or experiment subsets to consider

includeSubsets - include results from experiment subsets

sourceExperimentIdMap - a mapping of results to source experiment ID

experimentAnalyzedIdMap - a mapping of results to experiment analyzed ID

baselineMap - a mapping of results to baselines

threshold - a maximum threshold on the corrected P-value, between 0 and 1 inclusively

useGene2Cs - use the GENE2CS table, which is faster but may be inaccurate

keepNonSpecificProbes - whether to keep probes that map to more than one gene

initializeFactorValues - whether to initialize factor values in contrasts and baselines, note that their experimental factors will not be initialized

Returns:

differential expression results, grouped by analyzed experiment ID

findByGeneAndExperimentAnalyzed

public Map<BioAssaySet,List<DifferentialExpressionAnalysisResult>> findByGeneAndExperimentAnalyzed(Gene gene,
 boolean useGene2Cs,
 boolean keepNonSpecificProbes,
 Collection<Long> experimentAnalyzedIds,
 boolean includeSubsets,
 double threshold,
 int limit)

Description copied from interface: DifferentialExpressionResultDao

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 DifferentialExpressionResultDao

Parameters:

gene - gene

useGene2Cs - use the GENE2CS table, which is faster but may be inaccurate

keepNonSpecificProbes - keep non-specific probes

experimentAnalyzedIds - restrict results to analysis of these experiments

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

threshold - threshold

limit - limit

Returns:

map to diff ex VOs

findByExperimentAnalyzed

public Map<BioAssaySet,List<DifferentialExpressionAnalysisResult>> findByExperimentAnalyzed(Collection<Long> experimentAnalyzedIds,
 boolean includeSubSets,
 double threshold,
 int limit)

Description copied from interface: DifferentialExpressionResultDao

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 DifferentialExpressionResultDao

Parameters:

experimentAnalyzedIds - experiment analyzed IDs

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

threshold - threshold

limit - limit

Returns:

map to diff ex VOs

findByGene

public Map<BioAssaySet,List<DifferentialExpressionAnalysisResult>> findByGene(Gene gene,
 boolean useGene2Cs,
 boolean keepNonSpecificProbes)

Description copied from interface: DifferentialExpressionResultDao

Find differential expression results for a given gene, grouped by experiment.

Specified by:

findByGene in interface DifferentialExpressionResultDao

Parameters:

useGene2Cs - use the GENE2CS table, which is faster but may be inaccurate

keepNonSpecificProbes - keep non-specific probes

Returns:

a map of a collection of DifferentialExpressionAnalysisResults keyed by BioAssaySet.

findByGene

public Map<BioAssaySet,List<DifferentialExpressionAnalysisResult>> findByGene(Gene gene,
 boolean useGene2Cs,
 boolean keepNonSpecificProbes,
 double threshold,
 int limit)

Description copied from interface: DifferentialExpressionResultDao

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

Specified by:

findByGene in interface DifferentialExpressionResultDao

Parameters:

gene - gene

useGene2Cs - use the GENE2CS table, which is faster but may be inaccurate

keepNonSpecificProbes - keep non-specific probes (i.e. probes that map to more than one gene)

threshold - threshold

limit - limit

Returns:

map to diff exp VOs

findByGeneAndExperimentAnalyzed

public Map<BioAssaySet,List<DifferentialExpressionAnalysisResult>> findByGeneAndExperimentAnalyzed(Gene gene,
 boolean useGene2Cs,
 boolean keepNonSpecificProbes,
 Collection<Long> experimentAnalyzedIds,
 boolean includeSubSets)

Description copied from interface: DifferentialExpressionResultDao

Find differential expression results for a given gene and set of experiments, grouped by experiment.

Specified by:

findByGeneAndExperimentAnalyzed in interface DifferentialExpressionResultDao

Parameters:

gene - gene to retrieve differential expression for

useGene2Cs - use the GENE2CS table, which is faster but may be inaccurate

keepNonSpecificProbes - keep non-specific probes (i.e. probes that map to more than one gene)

experimentAnalyzedIds - IDs of experiments or experiment subsets to consider

includeSubSets - include subsets of the analyzed experiments

Returns:

a map of a collection of DifferentialExpressionAnalysisResults keyed by BioAssaySet.

findGeneResultsByResultSetIdsAndGeneIds

public Map<Long,Map<Long,DiffExprGeneSearchResult>> findGeneResultsByResultSetIdsAndGeneIds(Collection<DiffExResultSetSummaryValueObject> resultSets,
 Collection<Long> geneIds)

Description copied from interface: DifferentialExpressionResultDao

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

Specified by:

findGeneResultsByResultSetIdsAndGeneIds in interface DifferentialExpressionResultDao

Parameters:

resultSets - result sets

geneIds - gene IDs

Returns:

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

findByResultSet

public List<DifferentialExpressionValueObject> findByResultSet(ExpressionAnalysisResultSet resultSet,
 double threshold,
 int limit,
 int minNumberOfResults)

Specified by:

findByResultSet in interface DifferentialExpressionResultDao

findContrastsByAnalysisResultIds

public Map<Long,ContrastsValueObject> findContrastsByAnalysisResultIds(Collection<Long> ids)

Key method for getting contrasts associated with results.

Specified by:

findContrastsByAnalysisResultIds in interface DifferentialExpressionResultDao

Parameters:

ids - analysis result IDs

Returns:

map of result to contrasts value object.