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

Interface CoexpressionDao

All Known Implementing Classes:

CoexpressionDaoImpl

public interface CoexpressionDao

See Also:

• Gene2GeneCoexpression

Method Summary

Modifier and Type	Method	Description
Integer	countLinks(Gene gene, ExpressionExperiment ee)
Map<Gene,Integer>	countOldLinks(Collection<Gene> genes)
void	createOrUpdate(ExpressionExperiment bioAssaySet, List<NonPersistentNonOrderedCoexpLink> p2plinks, LinkCreator c, Set<Gene> genesTested)
void	deleteLinks(Taxon taxon, ExpressionExperiment experiment)
List<CoexpressionValueObject>	findCoexpressionRelationships(Gene gene, Collection<Long> bas, int maxResults, boolean quick)	Find coexpression links for a gene that are common to all the given datasets.
Map<Long,List<CoexpressionValueObject>>	findCoexpressionRelationships(Taxon taxon, Collection<Long> genes, Collection<Long> bas, int maxResults, boolean quick)	Find coexpression links for the genes that are common to all the given datasets, so stringency = bas.size().
Map<Long,List<CoexpressionValueObject>>	findCoexpressionRelationships(Taxon t, Collection<Long> genes, Collection<Long> bas, int stringency, int maxResults, boolean quick)
Map<Long,List<CoexpressionValueObject>>	findInterCoexpressionRelationships(Taxon taxon, Collection<Long> genes, Collection<Long> bas, int stringency, boolean quick)	Return coexpression relationships among the given genes, limited to the given data sets.
Collection<CoexpressionValueObject>	getCoexpression(Taxon taxon, ExpressionExperiment experiment, boolean quick)
boolean	hasLinks(Taxon taxon, ExpressionExperiment ee)
Map<SupportDetails,Gene2GeneCoexpression>	initializeFromOldData(Gene gene, Map<Long,Gene> geneIdMap, Map<NonPersistentNonOrderedCoexpLink,SupportDetails> linksSoFar, Set<Long> skipGenes)
int	queryAndCache(Gene gene)
GeneCoexpressionNodeDegreeValueObject	updateNodeDegree(Gene gene, GeneCoexpressionNodeDegree nd)	This is a maintenance method.
void	updateRelativeNodeDegrees(Map<Long,List<Double>> relRanksPerGenePos, Map<Long,List<Double>> relRanksPerGeneNeg)

Method Details

hasLinks

boolean hasLinks(Taxon taxon,
 ExpressionExperiment ee)

countLinks

Integer countLinks(Gene gene,
 ExpressionExperiment ee)

createOrUpdate

void createOrUpdate(ExpressionExperiment bioAssaySet,
 List<NonPersistentNonOrderedCoexpLink> p2plinks,
 LinkCreator c,
 Set<Gene> genesTested)

Parameters:

bioAssaySet - bio assay set

p2plinks - in gene order

c - link creator

genesTested - genes tested

deleteLinks

void deleteLinks(Taxon taxon,
 ExpressionExperiment experiment)

findCoexpressionRelationships

List<CoexpressionValueObject> findCoexpressionRelationships(Gene gene,
 Collection<Long> bas,
 int maxResults,
 boolean quick)

Find coexpression links for a gene that are common to all the given datasets. That is the stringency is bas.size().

Parameters:

gene - gene

bas - bio assays

maxResults - max results

quick - quick

Returns:

coexpression VO

findCoexpressionRelationships

Map<Long,List<CoexpressionValueObject>> findCoexpressionRelationships(Taxon taxon,
 Collection<Long> genes,
 Collection<Long> bas,
 int maxResults,
 boolean quick)

Find coexpression links for the genes that are common to all the given datasets, so stringency = bas.size().

Parameters:

taxon - taxon

genes - genes

bas - bio assays

maxResults - max results

quick - quick

Returns:

map of ids to coexp. VOs

findCoexpressionRelationships

Map<Long,List<CoexpressionValueObject>> findCoexpressionRelationships(Taxon t,
 Collection<Long> genes,
 Collection<Long> bas,
 int stringency,
 int maxResults,
 boolean quick)

Parameters:

t - taxon

genes - genes

bas - limit on which data sets to query, or null (or empty) for no limit.

stringency - minimum number of the datasets the link must be supported by

maxResults - maximum results per gene.

quick - quick

Returns:

map of ids to coexp. VOs

findInterCoexpressionRelationships

Map<Long,List<CoexpressionValueObject>> findInterCoexpressionRelationships(Taxon taxon,
 Collection<Long> genes,
 Collection<Long> bas,
 int stringency,
 boolean quick)

Return coexpression relationships among the given genes, limited to the given data sets.

Parameters:

taxon - taxon

genes - genes

bas - bio assays

stringency - stringency

quick - quick

Returns:

map of ids to coexp. VOs

updateNodeDegree

GeneCoexpressionNodeDegreeValueObject updateNodeDegree(Gene gene,
 GeneCoexpressionNodeDegree nd)

This is a maintenance method. This requires doing a coexpression query for the gene, and updating (or, if need be, creating) the associated GeneCoexpressionNodeDegree object.

Parameters:

gene - gene

nd - node degree

Returns:

updated value object

getCoexpression

Collection<CoexpressionValueObject> getCoexpression(Taxon taxon,
 ExpressionExperiment experiment,
 boolean quick)

Parameters:

taxon - taxon

experiment - experiment

quick - quick

Returns:

links, but not including flipped versions

queryAndCache

int queryAndCache(Gene gene)

Parameters:

gene - gene

Returns:

number of links that were cached

initializeFromOldData

Map<SupportDetails,Gene2GeneCoexpression> initializeFromOldData(Gene gene,
 Map<Long,Gene> geneIdMap,
 Map<NonPersistentNonOrderedCoexpLink,SupportDetails> linksSoFar,
 Set<Long> skipGenes)

countOldLinks

Map<Gene,Integer> countOldLinks(Collection<Gene> genes)

updateRelativeNodeDegrees

void updateRelativeNodeDegrees(Map<Long,List<Double>> relRanksPerGenePos,
 Map<Long,List<Double>> relRanksPerGeneNeg)