ubic.gemma.core.analysis.expression.coexpression

Class GeneCoexpressionSearchServiceImpl

java.lang.Object

ubic.gemma.core.analysis.expression.coexpression.GeneCoexpressionSearchServiceImpl

All Implemented Interfaces:

GeneCoexpressionSearchService

@Component
 @Lazy
public class GeneCoexpressionSearchServiceImpl
extends Object
implements GeneCoexpressionSearchService

Author:

paul

Constructor Summary

Constructors

Constructor and Description
GeneCoexpressionSearchServiceImpl(ExpressionExperimentService expressionExperimentService, CoexpressionService coexpressionService, CoexpressionAnalysisService coexpressionAnalysisService, GeneService geneService)

Method Summary

Modifier and Type	Method and Description
CoexpressionMetaValueObject	coexpressionSearch(Collection<Long> inputEeIds, Collection<Long> genes, int stringency, int maxResults, boolean queryGenesOnly)
CoexpressionMetaValueObject	coexpressionSearchQuick(Collection<Long> eeIds, Collection<Long> queryGenes, int stringency, int maxResults, boolean queryGenesOnly) Skips some of the postprocessing steps, use in situations where raw speed is more important than details.

Methods inherited from class java.lang.Object

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

Constructor Detail

GeneCoexpressionSearchServiceImpl

@Autowired
public GeneCoexpressionSearchServiceImpl(ExpressionExperimentService expressionExperimentService,
                                                    CoexpressionService coexpressionService,
                                                    CoexpressionAnalysisService coexpressionAnalysisService,
                                                    GeneService geneService)

Method Detail

coexpressionSearch

public CoexpressionMetaValueObject coexpressionSearch(Collection<Long> inputEeIds,
                                                      Collection<Long> genes,
                                                      int stringency,
                                                      int maxResults,
                                                      boolean queryGenesOnly)

Specified by:

coexpressionSearch in interface GeneCoexpressionSearchService

Parameters:

inputEeIds - Expression experiments ids to consider; if null, use all available data.

genes - Genes to find coexpression for

stringency - Minimum support level

maxResults - per gene

queryGenesOnly - Whether to return only coexpression among the query genes (assuming there are more than one). Otherwise, coexpression with genes 'external' to the queries will be returned.

Returns:

CoexpressionMetaValueObject in which the results are already populated and sorted.

coexpressionSearchQuick

public CoexpressionMetaValueObject coexpressionSearchQuick(Collection<Long> eeIds,
                                                           Collection<Long> queryGenes,
                                                           int stringency,
                                                           int maxResults,
                                                           boolean queryGenesOnly)

Description copied from interface: GeneCoexpressionSearchService

Skips some of the postprocessing steps, use in situations where raw speed is more important than details.

Specified by:

coexpressionSearchQuick in interface GeneCoexpressionSearchService

Parameters:

eeIds - Expression experiments ids to consider; if null or empty, use all available data.

queryGenes - genes

stringency - stringency

maxResults - max results

queryGenesOnly - query genes only

Returns:

CoexpressionMetaValueObject in which the results are already populated and sorted.