Package ubic.gemma.core.analysis.expression.coexpression

Interface GeneCoexpressionSearchService

All Known Implementing Classes:
GeneCoexpressionSearchServiceImpl
public interface GeneCoexpressionSearchService
Provides access to Gene2Gene links. The use of this service provides 'high-level' access to functionality in the Gene2GeneCoexpressionService.
Author:
Paul

  • Method Details

    • coexpressionSearch

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

      CoexpressionMetaValueObject coexpressionSearchQuick(Collection<Long> inputEeIds, Collection<Long> genes, int stringency, int maxResults, boolean queryGenesOnly)
      Skips some of the postprocessing steps, use in situations where raw speed is more important than details.
      Parameters:
      inputEeIds - Expression experiments ids to consider; if null or empty, use all available data.
      genes - genes
      stringency - stringency
      maxResults - max results
      queryGenesOnly - query genes only
      Returns:
      CoexpressionMetaValueObject in which the results are already populated and sorted.