Class GeneCoexpressionSearchServiceImpl
- java.lang.Object
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- ubic.gemma.core.analysis.expression.coexpression.GeneCoexpressionSearchServiceImpl
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- All Implemented Interfaces:
GeneCoexpressionSearchService
@Component @Lazy public class GeneCoexpressionSearchServiceImpl extends Object implements GeneCoexpressionSearchService
- Author:
- paul
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Constructor Summary
Constructors Constructor Description GeneCoexpressionSearchServiceImpl(ExpressionExperimentService expressionExperimentService, CoexpressionService coexpressionService, CoexpressionAnalysisService coexpressionAnalysisService, GeneService geneService)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method 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.
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Constructor Detail
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GeneCoexpressionSearchServiceImpl
@Autowired public GeneCoexpressionSearchServiceImpl(ExpressionExperimentService expressionExperimentService, CoexpressionService coexpressionService, CoexpressionAnalysisService coexpressionAnalysisService, GeneService geneService)
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Method Detail
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coexpressionSearch
public CoexpressionMetaValueObject coexpressionSearch(Collection<Long> inputEeIds, Collection<Long> genes, int stringency, int maxResults, boolean queryGenesOnly)
- Specified by:
coexpressionSearch
in interfaceGeneCoexpressionSearchService
- Parameters:
inputEeIds
- Expression experiments ids to consider; if null, use all available data.genes
- Genes to find coexpression forstringency
- Minimum support levelmaxResults
- per genequeryGenesOnly
- 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.
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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 interfaceGeneCoexpressionSearchService
- Parameters:
eeIds
- Expression experiments ids to consider; if null or empty, use all available data.queryGenes
- genesstringency
- stringencymaxResults
- max resultsqueryGenesOnly
- query genes only- Returns:
- CoexpressionMetaValueObject in which the results are already populated and sorted.
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