Package phase

Class Stage2Baum

java.lang.Object
phase.Stage2Baum
public class Stage2Baum extends Object

Class Stage2Baum applies the forward and backward algorithms for a haploid Li and Stephens hidden Markov model at high-frequency markers, and imputes missing genotypes and heterozygote phase at low-frequency markers.

Instances of class Stage2Baum are not thread-safe.

  • Constructor Details

    • Stage2Baum

      public Stage2Baum(LowFreqPhaseIbs phaseIbs, Stage2Haps stage2Haps)
      Creates a ImputeBaum instance from the specified data.
      Parameters:
      phaseIbs - the IBS haplotypes
      stage2Haps - an object for storing phased genotypes
      Throws:
      NullPointerException - if phaseIbs == null || stage2Haps == null

  • Method Details

    • nTargSamples

      public int nTargSamples()
      Returns the number of target samples.
      Returns:
      the number of target samples

    • phase

      public void phase(int targSample)
      Estimates and stores the phased haplotypes for the specified sample.
      Parameters:
      targSample - a sample index
      Throws:
      IndexOutOfBoundsException - if sample < 0 || sample >= this.nTargSamples()