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 Detail

      • 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
        maxResults - max results
        queryGenesOnly - query genes only
        stringency - stringency
        Returns:
        CoexpressionMetaValueObject in which the results are already populated and sorted.