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

Interface CoexpressionService

  • All Known Implementing Classes:
    CoexpressionServiceImpl
    public interface CoexpressionService
    A key service for working with coexpression at a fairly low level. This is responsible for CUD operations; retrieval is by 'find' methods. Note that all of the 'find' methods require a non-empty set of dataset ids to query. It is the responsibility of the caller to security-filter the ids. The need for security is why we don't permit queries of "all" data sets at this level. Retrieval of information on gene node degree is not constrained by security, which we deemed acceptable because the only information returned is a summary count.
    Author:
    Gemma

    • Method Detail

      • hasLinks

        boolean hasLinks​(BioAssaySet ee)
        Check if a given dataset has coexpression links.

      • countLinks

        @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Integer countLinks​(BioAssaySet ee,
                   Gene gene)
        Parameters:
        gene - gene
        ee - bio assay set
        Returns:
        the number of links the gene has in the given data set ("node degree")

      • createOrUpdate

        @Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
void createOrUpdate​(BioAssaySet bioAssaySet,
                    List<NonPersistentNonOrderedCoexpLink> links,
                    LinkCreator c,
                    Set<Gene> geesTested)
        Maintenance method.
        Parameters:
        bioAssaySet - should be all of them for the bioAssaySet (not a batch)
        geesTested - genes which were tested
        c - link creator
        links - links

      • deleteLinks

        @Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
void deleteLinks​(BioAssaySet experiment)
        Maintenance method. Remove coexpression information from the database about the experiment in question (this does not remove the analysis object).
        Parameters:
        experiment - experiment

      • findCoexpressionRelationships

        List<CoexpressionValueObject> findCoexpressionRelationships​(Gene gene,
                                                            Collection<Long> bas,
                                                            int maxResults,
                                                            boolean quick)
        Find links which are common to all of the given data sets.
        Parameters:
        bas - data sets the link must be supported by; that is, the stringency is implied by bas.size(). Assumed to be security-filtered.
        gene - gene
        quick - quick
        maxResults - max results
        Returns:
        coexpression results.

      • findCoexpressionRelationships

        List<CoexpressionValueObject> findCoexpressionRelationships​(Gene gene,
                                                            Collection<Long> bas,
                                                            int stringency,
                                                            int maxResults,
                                                            boolean quick)
        Search for coexpression across all available data sets, for the given genes considered individually, subject to a stringency constraint.
        Parameters:
        bas - assumed to be security-filtered.
        stringency - the minimum number of data sets for which the coexpression must be observed, among the given datasets.
        quick - quick
        maxResults - max results
        gene - gene
        Returns:
        coexpression results.

      • findCoexpressionRelationships

        Map<Long,​List<CoexpressionValueObject>> findCoexpressionRelationships​(Taxon t,
                                                                            Collection<Long> genes,
                                                                            Collection<Long> bas,
                                                                            int maxResults,
                                                                            boolean quick)
        Find coexpression links for the genes that are common to all the given datasets (that is, the stringency is equal to the size of the set of datasets)
        Parameters:
        bas - - assumed to already be security-filtered
        quick - quick
        maxResults - max results
        genes - genes
        t - taxon
        Returns:
        a map of gene IDs to coexpression results.

      • findCoexpressionRelationships

        Map<Long,​List<CoexpressionValueObject>> findCoexpressionRelationships​(Taxon t,
                                                                            Collection<Long> genes,
                                                                            Collection<Long> bas,
                                                                            int stringency,
                                                                            int maxResults,
                                                                            boolean quick)
        Find coexpression links for the genes that are common to at least stringency of the given datasets.
        Parameters:
        bas - assumed to already be security-filtered
        maxResults - limit to the number of results per gene, but connections among the query genes (if there is more than one) are given priority and not subject to the limit.
        stringency - the minimum number of data sets for which the coexpression must be observed, among the given datasets.
        quick - quick
        t - taxon
        genes - genes
        Returns:
        a map of gene IDs to coexpression results.

      • findInterCoexpressionRelationships

        Map<Long,​List<CoexpressionValueObject>> findInterCoexpressionRelationships​(Taxon t,
                                                                                 Collection<Long> genes,
                                                                                 Collection<Long> bas,
                                                                                 int stringency,
                                                                                 boolean quick)
        Return coexpression relationships among the given genes in the given data sets, in a map of query gene to coexpression objects.
        Parameters:
        bas - data sets to be considered, presumed to be security filtered already
        stringency - Must be less than or equal to the number of data sets datasets.
        quick - quick
        t - taxon
        genes - genes
        Returns:
        a map of gene IDs to coexpression results.

      • getCoexpression

        @Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Collection<CoexpressionValueObject> getCoexpression​(BioAssaySet experiment,
                                                    boolean quick)
        Parameters:
        quick - quick
        experiment - experiment
        Returns:
        all the coexpression links for the given experiment, but not including flipped versions

      • updateNodeDegrees

        @Secured("GROUP_ADMIN")
void updateNodeDegrees​(Taxon taxon)