Package ubic.gemma.persistence.service.association.coexpression

Class CoexpressionServiceImpl

java.lang.Object

ubic.gemma.persistence.service.association.coexpression.CoexpressionServiceImpl

All Implemented Interfaces:

CoexpressionService

@Service
public class CoexpressionServiceImpl
extends Object
implements CoexpressionService

See Also:

• CoexpressionService

Constructor Summary

Constructors

Constructor	Description
CoexpressionServiceImpl()

Method Summary

Modifier and Type	Method	Description
Integer	countLinks(ExpressionExperiment ee, Gene gene)
Map<Gene,Integer>	countOldLinks(Collection<Gene> genes)
void	createOrUpdate(ExpressionExperiment ee, List<NonPersistentNonOrderedCoexpLink> links, LinkCreator c, Set<Gene> genesTested)	Maintenance method.
void	deleteLinks(ExpressionExperiment experiment)	Maintenance method.
List<CoexpressionValueObject>	findCoexpressionRelationships(Gene gene, Collection<Long> bas, int maxResults, boolean quick)	Find links which are common to all of the given data sets.
List<CoexpressionValueObject>	findCoexpressionRelationships(Gene gene, Collection<Long> bas, int stringency, int maxResults, boolean quick)	Search for coexpression across all available data sets, for the given genes considered individually, subject to a stringency constraint.
Map<Long,List<CoexpressionValueObject>>	findCoexpressionRelationships(Taxon t, Collection<Long> genes, Collection<Long> bas, int maxResults, boolean quick)	Find coexpression links for the genes that are common to all the given datasets (that is, the stringency is equal to the size of the set of datasets)
Map<Long,List<CoexpressionValueObject>>	findCoexpressionRelationships(Taxon t, Collection<Long> genes, Collection<Long> bas, int stringency, int maxResults, boolean quick)	Find coexpression links for the genes that are common to at least stringency of the given datasets.
Map<Long,List<CoexpressionValueObject>>	findInterCoexpressionRelationships(Taxon t, Collection<Long> genes, Collection<Long> bas, int stringency, boolean quick)	Return coexpression relationships among the given genes in the given data sets, in a map of query gene to coexpression objects.
Collection<CoexpressionValueObject>	getCoexpression(ExpressionExperiment experiment, boolean quick)
GeneCoexpressionNodeDegreeValueObject	getNodeDegree(Gene g)
Map<Long,GeneCoexpressionNodeDegreeValueObject>	getNodeDegrees(Collection<Long> g)
boolean	hasLinks(ExpressionExperiment ee)	Check if a given dataset has coexpression links.
Map<SupportDetails,Gene2GeneCoexpression>	initializeLinksFromOldData(Gene g, Map<Long,Gene> idMap, Map<NonPersistentNonOrderedCoexpLink,SupportDetails> linksSoFar, Set<Long> skipGenes)
void	updateNodeDegrees(Taxon t)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

CoexpressionServiceImpl

public CoexpressionServiceImpl()

Method Details

hasLinks

public boolean hasLinks(ExpressionExperiment ee)

Description copied from interface: CoexpressionService

Check if a given dataset has coexpression links.

Specified by:

hasLinks in interface CoexpressionService

countLinks

@Transactional(readOnly=true)
public Integer countLinks(ExpressionExperiment ee,
 Gene gene)

Specified by:

countLinks in interface CoexpressionService

Parameters:

ee - bio assay set

gene - gene

Returns:

the number of links the gene has in the given data set ("node degree")

createOrUpdate

@Transactional
public void createOrUpdate(ExpressionExperiment ee,
 List<NonPersistentNonOrderedCoexpLink> links,
 LinkCreator c,
 Set<Gene> genesTested)

Description copied from interface: CoexpressionService

Maintenance method.

Specified by:

createOrUpdate in interface CoexpressionService

Parameters:

ee - should be all of them for the bioAssaySet (not a batch)

links - links

c - link creator

genesTested - genes which were tested

deleteLinks

@Transactional
public void deleteLinks(ExpressionExperiment experiment)

Description copied from interface: CoexpressionService

Maintenance method. Remove coexpression information from the database about the experiment in question (this does not remove the analysis object).

Specified by:

deleteLinks in interface CoexpressionService

Parameters:

experiment - experiment

findCoexpressionRelationships

@Transactional(readOnly=true)
public List<CoexpressionValueObject> findCoexpressionRelationships(Gene gene,
 Collection<Long> bas,
 int maxResults,
 boolean quick)

Description copied from interface: CoexpressionService

Find links which are common to all of the given data sets.

Specified by:

findCoexpressionRelationships in interface CoexpressionService

Parameters:

gene - gene

bas - data sets the link must be supported by; that is, the stringency is implied by bas.size(). Assumed to be security-filtered.

maxResults - max results

quick - quick

Returns:

coexpression results.

findCoexpressionRelationships

@Transactional(readOnly=true)
public List<CoexpressionValueObject> findCoexpressionRelationships(Gene gene,
 Collection<Long> bas,
 int stringency,
 int maxResults,
 boolean quick)

Description copied from interface: CoexpressionService

Search for coexpression across all available data sets, for the given genes considered individually, subject to a stringency constraint.

Specified by:

findCoexpressionRelationships in interface CoexpressionService

Parameters:

gene - gene

bas - assumed to be security-filtered.

stringency - the minimum number of data sets for which the coexpression must be observed, among the given datasets.

maxResults - max results

quick - quick

Returns:

coexpression results.

findCoexpressionRelationships

@Transactional(readOnly=true)
public Map<Long,List<CoexpressionValueObject>> findCoexpressionRelationships(Taxon t,
 Collection<Long> genes,
 Collection<Long> bas,
 int maxResults,
 boolean quick)

Description copied from interface: CoexpressionService

Find coexpression links for the genes that are common to all the given datasets (that is, the stringency is equal to the size of the set of datasets)

Specified by:

findCoexpressionRelationships in interface CoexpressionService

Parameters:

t - taxon

genes - genes

bas - - assumed to already be security-filtered

maxResults - max results

quick - quick

Returns:

a map of gene IDs to coexpression results.

findCoexpressionRelationships

@Transactional(readOnly=true)
public Map<Long,List<CoexpressionValueObject>> findCoexpressionRelationships(Taxon t,
 Collection<Long> genes,
 Collection<Long> bas,
 int stringency,
 int maxResults,
 boolean quick)

Description copied from interface: CoexpressionService

Find coexpression links for the genes that are common to at least stringency of the given datasets.

Specified by:

findCoexpressionRelationships in interface CoexpressionService

Parameters:

t - taxon

genes - genes

bas - assumed to already be security-filtered

stringency - the minimum number of data sets for which the coexpression must be observed, among the given datasets.

maxResults - limit to the number of results per gene, but connections among the query genes (if there is more than one) are given priority and not subject to the limit.

quick - quick

Returns:

a map of gene IDs to coexpression results.

findInterCoexpressionRelationships

@Transactional(readOnly=true)
public Map<Long,List<CoexpressionValueObject>> findInterCoexpressionRelationships(Taxon t,
 Collection<Long> genes,
 Collection<Long> bas,
 int stringency,
 boolean quick)

Description copied from interface: CoexpressionService

Return coexpression relationships among the given genes in the given data sets, in a map of query gene to coexpression objects.

Specified by:

findInterCoexpressionRelationships in interface CoexpressionService

Parameters:

t - taxon

genes - genes

bas - data sets to be considered, presumed to be security filtered already

stringency - Must be less than or equal to the number of data sets datasets.

quick - quick

Returns:

a map of gene IDs to coexpression results.

getCoexpression

@Transactional(readOnly=true)
public Collection<CoexpressionValueObject> getCoexpression(ExpressionExperiment experiment,
 boolean quick)

Specified by:

getCoexpression in interface CoexpressionService

Parameters:

experiment - experiment

quick - quick

Returns:

all the coexpression links for the given experiment, but not including flipped versions

updateNodeDegrees

@Transactional
public void updateNodeDegrees(Taxon t)

Specified by:

updateNodeDegrees in interface CoexpressionService

getNodeDegree

@Transactional(readOnly=true)
public GeneCoexpressionNodeDegreeValueObject getNodeDegree(Gene g)

Specified by:

getNodeDegree in interface CoexpressionService

getNodeDegrees

@Transactional(readOnly=true)
public Map<Long,GeneCoexpressionNodeDegreeValueObject> getNodeDegrees(Collection<Long> g)

Specified by:

getNodeDegrees in interface CoexpressionService

initializeLinksFromOldData

@Transactional
public Map<SupportDetails,Gene2GeneCoexpression> initializeLinksFromOldData(Gene g,
 Map<Long,Gene> idMap,
 Map<NonPersistentNonOrderedCoexpLink,SupportDetails> linksSoFar,
 Set<Long> skipGenes)

Specified by:

initializeLinksFromOldData in interface CoexpressionService

Parameters:

g - gene

idMap - id map

linksSoFar - links so far

skipGenes - skip genes

Returns:

links that were made

countOldLinks

@Transactional(readOnly=true)
public Map<Gene,Integer> countOldLinks(Collection<Gene> genes)

Specified by:

countOldLinks in interface CoexpressionService