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

Class SampleCoexpressionAnalysis

  • All Implemented Interfaces:
    gemma.gsec.model.Securable, gemma.gsec.model.SecuredChild, Securable, SecuredChild, Describable, Identifiable
    public class SampleCoexpressionAnalysis
extends SingleExperimentAnalysis
    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 Detail

      • SampleCoexpressionAnalysis

        public SampleCoexpressionAnalysis()

    • Method Detail

      • 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.

      • 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