Package ubic.gemma.model.analysis.expression.coexpression

Class SampleCoexpressionAnalysis

java.lang.Object
ubic.gemma.model.common.AbstractIdentifiable
ubic.gemma.model.common.AbstractDescribable
ubic.gemma.model.analysis.Analysis
ubic.gemma.model.analysis.expression.ExpressionAnalysis
ubic.gemma.model.analysis.SingleExperimentAnalysis<ExpressionExperiment>
ubic.gemma.model.analysis.expression.coexpression.SampleCoexpressionAnalysis
All Implemented Interfaces:
gemma.gsec.model.Securable, gemma.gsec.model.SecuredChild, Securable, SecuredChild, Describable, Identifiable
public class SampleCoexpressionAnalysis extends SingleExperimentAnalysis<ExpressionExperiment>
The 'analysis' in the name is a bit of a stretch here, as this object servers purely as an aggregator of all the sample coexpression matrices.

  • Constructor Details

    • SampleCoexpressionAnalysis

      public SampleCoexpressionAnalysis()

  • Method Details

    • getFullCoexpressionMatrix

      public SampleCoexpressionMatrix getFullCoexpressionMatrix()
      Note that since you get a full square matrix, all correlations are represented twice, and values on the main diagonal will always be 1.
      Returns:
      a coexpression matrix with all factors (none regressed out), and including outliers.

    • setFullCoexpressionMatrix

      public void setFullCoexpressionMatrix(SampleCoexpressionMatrix rawFullCoexpressionMatrix)

    • getRegressedCoexpressionMatrix

      @Nullable public SampleCoexpressionMatrix getRegressedCoexpressionMatrix()
      Note that since you get a full square matrix, all correlations are represented twice, and values on the main diagonal will always be 1.
      Returns:
      a coexpression matrix with regressed out major factors.

    • setRegressedCoexpressionMatrix

      public void setRegressedCoexpressionMatrix(@Nullable SampleCoexpressionMatrix regressedCoexpressionMatrix)

    • getBestCoexpressionMatrix

      public SampleCoexpressionMatrix getBestCoexpressionMatrix()

    • equals

      public boolean equals(Object object)
      Description copied from class: AbstractIdentifiable
      Important note: Two objects with the same class and non-null ID must be considered equal. If one or both IDs are nulls, the rest of the state can be used to determine equality.
      Specified by:
      equals in class AbstractIdentifiable