Package ubic.gemma.core.analysis.preprocess.svd

Class SVDResult

java.lang.Object
ubic.gemma.core.analysis.preprocess.svd.SVDResult
All Implemented Interfaces:
Serializable
public final class SVDResult extends Object implements Serializable
Store information about SVD of expression data and comparisons to factors/batch information.
Author:
paul
See Also:

  • Constructor Details

  • Method Details

    • getExperimentAnalyzed

      public ExpressionExperiment getExperimentAnalyzed()
      Experiment or subset this is for.

    • getBioAssays

      public List<BioAssay> getBioAssays()
      Assays used in the SVD analysis.

      In order like the rows of the V matrix.

    • getBioMaterials

      public List<BioMaterial> getBioMaterials()
      Biomaterials used in the SVD analysis.

      In order like the rows of the V matrix.

    • getVariances

      public double[] getVariances()
      An array of values representing the fraction of the variance each component accounts for

    • getVMatrix

      public DoubleMatrix<BioMaterial,Integer> getVMatrix()
      Row names: biomaterials; column names: eigengene number (from 0)

    • getDates

      public List<Date> getDates()
      Date associated to the bioMaterials.

      Missing values are encoded as null.

    • getDateCorrelations

      public Map<Integer,Double> getDateCorrelations()
      Map of component to correlation that component with "batch/scan date"
      See Also:
      • dates

    • getDatePVals

      public Map<Integer,Double> getDatePVals()
      P-values associated to the "batch/scan date" component.
      See Also:
      • dates

    • getFactors

      public Map<ExperimentalFactor,List<Number>> getFactors()
      Map of factors to the double-ized representations of them.

    • getFactorCorrelations

      public Map<Integer,Map<ExperimentalFactor,Double>> getFactorCorrelations()
      Map of component to a map of ExperimentalFactor IDs to correlations of that factor with the component.

    • getFactorPVals

      public Map<Integer,Map<ExperimentalFactor,Double>> getFactorPVals()
      Map of component to map of ExperimentalFactor IDs to P-values for the association of that factor with the component.

      Need to store the correlations of eigengenes with dates of assays, and also with factors. Statistics are rank-based correlations

    • equals

      public boolean equals(Object o)
      Overrides:
      equals in class Object

    • hashCode

      public int hashCode()
      Overrides:
      hashCode in class Object

    • toString

      public String toString()
      Overrides:
      toString in class Object