Package imp

Class ImpIbs

java.lang.Object
imp.ImpIbs
public final class ImpIbs extends Object

Class ImpIbs identifies haplotypes that share a long IBS segment with a specified haplotype.

Instances of ImpIbs are immutable.

  • Constructor Summary

    Constructors
    Constructor
    Description
    ImpIbs(ImpData impData)
    Constructs a new ImpIbs object from the specified data.

  • Method Summary

    Modifier and Type
    Method
    Description
    CodedSteps
    codedSteps()
    Returns the coded steps.
    int[]
    ibsHaps(int hap, int step)
    Returns an array containing reference haplotype indices that that are IBS with the specified target haplotype in an interval beginning with the specified step.
    ImpData
    impData()
    Return the data for genotype imputation in the marker window.

    Methods inherited from class java.lang.Object

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

  • Constructor Details

    • ImpIbs

      public ImpIbs(ImpData impData)
      Constructs a new ImpIbs object from the specified data.
      Parameters:
      impData - the input data for genotype imputation
      Throws:
      NullPointerException - if impData == null

  • Method Details

    • ibsHaps

      public int[] ibsHaps(int hap, int step)
      Returns an array containing reference haplotype indices that that are IBS with the specified target haplotype in an interval beginning with the specified step. The returned array will contain fewer than this.nHapsPerStep() haplotypes if the number of reference haplotypes that are IBS with specified target haplotype in the specified step is less than this.nHapsPerStep().
      Parameters:
      hap - a haplotype index
      step - a step index
      Returns:
      an array containing reference haplotype indices that that are IBS with the specified target haplotype
      Throws:
      IndexOutOfBoundsException - if hap < 0 || hap >= this.hapPairs().nHaps()
      IndexOutOfBoundsException - if step < 0 || step >= this.nSteps()

    • impData

      public ImpData impData()
      Return the data for genotype imputation in the marker window.
      Returns:
      the data for genotype imputation in the marker window

    • codedSteps

      public CodedSteps codedSteps()
      Returns the coded steps. The coded steps stores the starting marker for each step along with the index of the allele sequence carried by each haplotype in each step.
      Returns:
      the coded steps