Package phase

Class ParamEstimates

java.lang.Object
phase.ParamEstimates
public class ParamEstimates extends Object

Class ParamEstimates estimates the allele mismatch probability and the recombination intensity for a haploid Li and Stephens hidden Markov model.

Instances of class ParamEstimates are thread-safe.

  • Constructor Summary

    Constructors
    Constructor
    Description
    ParamEstimates()
    Constructs a new ParamEstimates instance for the specified data.

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    addMismatchData(int markerCnt, double pMismatchSum)
    Records the specified allele mismatch data if markerCnt and pMismatchSum are finite positive values.
    void
    addSwitchData(double genDistances, double switchProbs)
    Records the specified genetic distance and switch probability if genDistances and switchProbs are finite positive values.
    void
    clear()
    Clears all data that has been added via the this.addMismatchData and this.addSwitchData() methods.
    float
    pMismatch()
    Returns the estimated allele mismatch rate.
    float
    recombIntensity()
    Returns the estimated recombination intensities.

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

  • Constructor Details

    • ParamEstimates

      public ParamEstimates()
      Constructs a new ParamEstimates instance for the specified data.

  • Method Details

    • addMismatchData

      public void addMismatchData(int markerCnt, double pMismatchSum)
      Records the specified allele mismatch data if markerCnt and pMismatchSum are finite positive values.
      Parameters:
      markerCnt - the number of markers with mismatch data
      pMismatchSum - the sum of estimated allele mismatch probabilities

    • addSwitchData

      public void addSwitchData(double genDistances, double switchProbs)
      Records the specified genetic distance and switch probability if genDistances and switchProbs are finite positive values.
      Parameters:
      genDistances - the list of genetic distance
      switchProbs - the list of haplotype switch probabilities

    • pMismatch

      public float pMismatch()
      Returns the estimated allele mismatch rate. Returns Float.NaN if there is no data to estimate the allele mismatch rate. The returned value is not an atomic snapshot. Invocation in the absence of concurrent update will return an accurate result, but concurrent updates that occur white the sum is being calculated might not be incorporated in the returned result.
      Returns:
      the estimated allele mismatch rate

    • recombIntensity

      public float recombIntensity()
      Returns the estimated recombination intensities. Returns Float.NaN if there is no data from which to estimate recombination intensities. The returned value is NOT an atomic snapshot. An accurate result is guaranteed only if no concurrent updates occur during method invocation.
      Returns:
      the estimated recombination intensities

    • clear

      public void clear()
      Clears all data that has been added via the this.addMismatchData and this.addSwitchData() methods.