Package ubic.gemma.persistence.service.analysis.expression.diff

Interface DifferentialExpressionResultDao

All Superinterfaces:
BaseDao<DifferentialExpressionAnalysisResult>
All Known Implementing Classes:
DifferentialExpressionResultDaoImpl
public interface DifferentialExpressionResultDao extends BaseDao<DifferentialExpressionAnalysisResult>
See Also:

  • Method Details

    • findByGene

      Map<BioAssaySet,List<DifferentialExpressionAnalysisResult>> findByGene(Gene gene, boolean useGene2Cs, boolean keepNonSpecificProbes)
      Find differential expression results for a given gene, grouped by experiment.
      Parameters:
      useGene2Cs - use the GENE2CS table, which is faster but may be inaccurate
      keepNonSpecificProbes - keep non-specific probes
      Returns:
      a map of a collection of DifferentialExpressionAnalysisResults keyed by BioAssaySet.

    • findByGene

      Map<BioAssaySet,List<DifferentialExpressionAnalysisResult>> findByGene(Gene gene, boolean useGene2Cs, boolean keepNonSpecificProbes, double threshold, int limit)
      Find differential expression for a gene, exceeding a given significance level (using the corrected pvalue field)
      Parameters:
      gene - gene
      useGene2Cs - use the GENE2CS table, which is faster but may be inaccurate
      keepNonSpecificProbes - keep non-specific probes (i.e. probes that map to more than one gene)
      threshold - threshold
      limit - limit
      Returns:
      map to diff exp VOs

    • findByExperimentAnalyzed

      Map<BioAssaySet,List<DifferentialExpressionAnalysisResult>> findByExperimentAnalyzed(Collection<Long> experimentAnalyzedIds, boolean includeSubSets, double threshold, int limit)
      Given a list of experiments and a threshold value finds all the probes that met the cut-off in the given experiments
      Parameters:
      experimentAnalyzedIds - experiment analyzed IDs
      includeSubSets - if true, include the subsets of the experiments analyzed
      threshold - threshold
      limit - limit
      Returns:
      map to diff ex VOs

    • findByGeneAndExperimentAnalyzed

      List<DifferentialExpressionAnalysisResult> findByGeneAndExperimentAnalyzed(Gene gene, Collection<Long> experimentAnalyzedIds, boolean includeSubsets, @Nullable Map<DifferentialExpressionAnalysisResult,Long> sourceExperimentIdMap, @Nullable Map<DifferentialExpressionAnalysisResult,Long> experimentAnalyzedIdMap, @Nullable Map<DifferentialExpressionAnalysisResult,Baseline> baselineMap, double threshold, boolean useGene2Cs, boolean keepNonSpecificProbes, boolean initializeFactorValues)
      Retrieve differential expression results for a given gene across all the given datasets.

      Results are grouped by result set. If a gene maps to more than one probe, the result with the lowest corrected P-value is selected.

      Parameters:
      gene - a specific gene to retrieve differential expression for
      experimentAnalyzedIds - list of IDs of experiments or experiment subsets to consider
      includeSubsets - include results from experiment subsets
      sourceExperimentIdMap - a mapping of results to source experiment ID
      experimentAnalyzedIdMap - a mapping of results to experiment analyzed ID
      baselineMap - a mapping of results to baselines
      threshold - a maximum threshold on the corrected P-value, between 0 and 1 inclusively
      useGene2Cs - use the GENE2CS table, which is faster but may be inaccurate
      keepNonSpecificProbes - whether to keep probes that map to more than one gene
      initializeFactorValues - whether to initialize factor values in contrasts and baselines, note that their experimental factors will not be initialized
      Returns:
      differential expression results, grouped by analyzed experiment ID

    • findByGeneAndExperimentAnalyzed

      Map<BioAssaySet,List<DifferentialExpressionAnalysisResult>> findByGeneAndExperimentAnalyzed(Gene gene, boolean useGene2Cs, boolean keepNonSpecificProbes, Collection<Long> experimentAnalyzedIds, boolean includeSubSets)
      Find differential expression results for a given gene and set of experiments, grouped by experiment.
      Parameters:
      gene - gene to retrieve differential expression for
      useGene2Cs - use the GENE2CS table, which is faster but may be inaccurate
      keepNonSpecificProbes - keep non-specific probes (i.e. probes that map to more than one gene)
      experimentAnalyzedIds - IDs of experiments or experiment subsets to consider
      includeSubSets - include subsets of the analyzed experiments
      Returns:
      a map of a collection of DifferentialExpressionAnalysisResults keyed by BioAssaySet.

    • findByGeneAndExperimentAnalyzed

      Map<BioAssaySet,List<DifferentialExpressionAnalysisResult>> findByGeneAndExperimentAnalyzed(Gene gene, boolean useGene2Cs, boolean keepNonSpecificProbes, Collection<Long> experimentsAnalyzed, boolean includeSubSets, double threshold, int limit)
      Find differential expression for a gene in given data sets, exceeding a given significance level (using the corrected pvalue field)
      Parameters:
      gene - gene
      useGene2Cs - use the GENE2CS table, which is faster but may be inaccurate
      keepNonSpecificProbes - keep non-specific probes
      experimentsAnalyzed - restrict results to analysis of these experiments
      includeSubSets - if true, include the subsets of the experiments analyzed
      threshold - threshold
      limit - limit
      Returns:
      map to diff ex VOs

    • findGeneResultsByResultSetIdsAndGeneIds

      Map<Long,Map<Long,DiffExprGeneSearchResult>> findGeneResultsByResultSetIdsAndGeneIds(Collection<DiffExResultSetSummaryValueObject> resultSets, Collection<Long> geneIds)
      Retrieve differential expression results in bulk. This is an important method for the differential expression interfaces.
      Parameters:
      resultSets - result sets
      geneIds - gene IDs
      Returns:
      map of resultset IDs to map of gene id to differential expression results.

    • findByResultSet

      List<DifferentialExpressionValueObject> findByResultSet(ExpressionAnalysisResultSet resultSet, double threshold, int maxResultsToReturn, int minNumberOfResults)

    • findContrastsByAnalysisResultIds

      Map<Long,ContrastsValueObject> findContrastsByAnalysisResultIds(Collection<Long> ids)
      Find contrast results by analysis result IDs.
      Parameters:
      ids - analysis result IDs
      Returns:
      map of result to contrasts value object.