Package ubic.gemma.model.analysis.expression.diff

Class ExpressionAnalysisResultSet

java.lang.Object
ubic.gemma.model.analysis.AnalysisResultSet<DifferentialExpressionAnalysisResult>
ubic.gemma.model.analysis.expression.FactorAssociatedAnalysisResultSet<DifferentialExpressionAnalysisResult>
ubic.gemma.model.analysis.expression.diff.ExpressionAnalysisResultSet
All Implemented Interfaces:
gemma.gsec.model.Securable, gemma.gsec.model.SecuredChild, Securable, SecuredChild<DifferentialExpressionAnalysis>, Identifiable
public class ExpressionAnalysisResultSet extends FactorAssociatedAnalysisResultSet<DifferentialExpressionAnalysisResult> implements SecuredChild<DifferentialExpressionAnalysis>
A group of results for an ExpressionExperiment.

  • Constructor Details

    • ExpressionAnalysisResultSet

      public ExpressionAnalysisResultSet()

  • Method Details

    • getAnalysis

      public DifferentialExpressionAnalysis getAnalysis()

    • setAnalysis

      public void setAnalysis(DifferentialExpressionAnalysis analysis)

    • getBaselineGroup

      @Nullable public FactorValue getBaselineGroup()
      Returns:
      The group considered baseline when computing scores and 'upRegulated'. This might be a control group if it could be recognized. For continuous factors, this would be null. For interaction terms we do not compute this so it will also be null.

    • setBaselineGroup

      public void setBaselineGroup(@Nullable FactorValue baselineGroup)

    • getHitListSizes

      public Set<HitListSize> getHitListSizes()

    • setHitListSizes

      public void setHitListSizes(Set<HitListSize> hitListSizes)

    • getNumberOfGenesTested

      public Integer getNumberOfGenesTested()
      Returns:
      How many genes were tested in the result set. This is determined based on the annotations at one point in time, so might slightly differ if the platform annotations have been updated since.

    • setNumberOfGenesTested

      public void setNumberOfGenesTested(Integer numberOfGenesTested)

    • getNumberOfProbesTested

      public Integer getNumberOfProbesTested()
      Returns:
      How many probes were tested in this result set.

    • setNumberOfProbesTested

      public void setNumberOfProbesTested(Integer numberOfProbesTested)

    • getPvalueDistribution

      public PvalueDistribution getPvalueDistribution()

    • setPvalueDistribution

      public void setPvalueDistribution(PvalueDistribution pvalueDistribution)

    • getResults

      public Set<DifferentialExpressionAnalysisResult> getResults()

    • setResults

      public void setResults(Set<DifferentialExpressionAnalysisResult> results)

    • getSecurityOwner

      public DifferentialExpressionAnalysis getSecurityOwner()
      Description copied from interface: SecuredChild
      Obtain the security owner of this secured child.

      Secured children should always have an owner in the ACL table, but that relation is not always direct or mapped. A more robust way of checking is to look up the parent via AclObjectIdentity.getParentObject(). If the security owner cannot be determined, the implementation should define a setter so it can be temporarily assigned for creating the ACL identity.

      Specified by:
      getSecurityOwner in interface gemma.gsec.model.SecuredChild
      Specified by:
      getSecurityOwner in interface SecuredChild<DifferentialExpressionAnalysis>
      Returns:
      the security owner, or null if not known.

    • toString

      public String toString()
      Overrides:
      toString in class Object