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

Interface MatrixRowPairAnalysis

All Known Implementing Classes:
AbstractMatrixRowPairAnalysis, PearsonMetrics, SpearmanMetrics
public interface MatrixRowPairAnalysis
Author:
Paul Pavlidis

  • Field Details

  • Method Details

    • calculateMetrics

      void calculateMetrics()

    • getHistogramArrayList

      DoubleArrayList getHistogramArrayList()

    • getKeepers

      ObjectArrayList getKeepers()

    • getMetricType

      QuantitationType getMetricType()

    • getProbeForRow

      CompositeSequence getProbeForRow(ExpressionDataMatrixRowElement rowEl)

    • getScoreInBin

      double getScoreInBin(int i)

    • numCached

      int numCached()

    • setDuplicateMap

      void setDuplicateMap(Map<CompositeSequence,Set<Gene>> probeToGeneMap)

    • setLowerTailThreshold

      void setLowerTailThreshold(double k)

    • setMinNumpresent

      void setMinNumpresent(int minSamplesToKeepCorrelation)

    • setOmitNegativeCorrelationLinks

      void setOmitNegativeCorrelationLinks(boolean omitNegativeCorrelationLinks)

    • setPValueThreshold

      void setPValueThreshold(double k)

    • setUpperTailThreshold

      void setUpperTailThreshold(double k)

    • setUseAbsoluteValue

      void setUseAbsoluteValue(boolean k)

    • setUsePvalueThreshold

      void setUsePvalueThreshold(boolean useIt)
      Default is true; set to false to disable use of the pvalue threshold, in which case only the upper and lower tail thresholds will be used.
      Parameters:
      useIt - new value

    • getCrossHybridizationRejections

      long getCrossHybridizationRejections()
      Use after analysis.
      Returns:
      how many pairs were rejected due to cross-hybridization potential

    • getNumUniqueGenes

      double getNumUniqueGenes()

    • size

      int size()
      Returns:
      how many rows/columns the matrix has.