Package ubic.gemma.core.analysis.expression.coexpression.links

Class LinkAnalysis

java.lang.Object
ubic.gemma.core.analysis.expression.coexpression.links.LinkAnalysis
public class LinkAnalysis extends Object
Handles the actual coexpression analysis, once handed data that has been prepared. Results are made available at the end. See LinkAnalysisCli for more instructions. This should be created for each analysis - it's not reusable.
Author:
xiangwan, paul (refactoring)

  • Field Details

    • log

      protected static final org.apache.commons.logging.Log log

  • Constructor Details

  • Method Details

    • analyze

      public void analyze()
      Main entry point.

    • clear

      public void clear()
      Clear/null data so this object can be reused.

    • getAnalysisObj

      public CoexpressionAnalysis getAnalysisObj()
      Returns:
      object containing the parameters used.

    • setAnalysisObj

      public void setAnalysisObj(CoexpressionAnalysis analysis)

    • getConfig

      public LinkAnalysisConfig getConfig()

    • getCorrelationDistribution

      public CoexpCorrelationDistribution getCorrelationDistribution()

    • getDataMatrix

      public ExpressionDataDoubleMatrix getDataMatrix()

    • setDataMatrix

      public void setDataMatrix(ExpressionDataDoubleMatrix paraDataMatrix)

    • getExpressionExperiment

      public ExpressionExperiment getExpressionExperiment()

    • setExpressionExperiment

      public void setExpressionExperiment(ExpressionExperiment expressionExperiment)

    • getGenesTested

      public Set<Gene> getGenesTested()
      Gene the genes that were tested, according to the rows that are currently in the dataMatrix (so call this after filtering!)
      Returns:
      set

    • getKeep

      public ObjectArrayList getKeep()

    • getMetric

      public QuantitationType getMetric()

    • getMetricMatrix

      public MatrixRowPairAnalysis getMetricMatrix()

    • getProbe

      public CompositeSequence getProbe(int index)

    • getProbeDegree

      public Integer getProbeDegree(int index)
      Parameters:
      index - row number in the metrixMatirx
      Returns:
      how many Links that probe appears in, or null if the probeDegree has not been populated for that index (that is, either to early to check, or it was zero).

    • getProbeToGeneMap

      public Map<CompositeSequence,Set<Gene>> getProbeToGeneMap()

    • setProbeToGeneMap

      public void setProbeToGeneMap(Map<CompositeSequence,Set<Gene>> probeToGeneMap)
      Once set, is unmodifiable.
      Parameters:
      probeToGeneMap - map

    • getTaxon

      public Taxon getTaxon()

    • setTaxon

      public void setTaxon(Taxon taxon)