Package phase

Class Ibs2

  • public final class Ibs2
extends java.lang.Object

    Class Ibs2 stores IBS2 segments that any target sample shares with another target sample.

    Instances of Ibs2 are immutable.

    • Constructor Summary

      Constructors 
      Constructor Description
      Ibs2​(GT targGT, MarkerMap map, FloatArray maf)
      Constructs a new Ibs2 instance from the specified data.

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      boolean areIbs2​(int targSample, int otherSample, int marker)
      Returns true if (otherSample < this.nTargSamples() and the specified samples are estimated to be IBS2 at the specified marker, and returns false otherwise.
      boolean areIbs2​(int targSample, int otherSample, int start, int inclEnd)
      Returns true if (0 <= otherSample && otherSample < this.nTargSamples()) and the specified samples are estimated to be IBS2 within the specified interval and returns false otherwise.
      int nIbs2Segments​(int targSample)
      Returns the number of IBS2 segments for the specified target sample
      int nMarkers()
      Returns the number of markers.
      int nTargSamples()
      Returns the number of target samples.

      • Methods inherited from class java.lang.Object

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

    • Constructor Detail

      • Ibs2

        public Ibs2​(GT targGT,
            MarkerMap map,
            FloatArray maf)
        Constructs a new Ibs2 instance from the specified data.
        Parameters:
        targGT - the target genotype data
        map - a list whose j-th element is the genetic map position of the j-th the marker
        maf - a list whose j-th element is the estimated minor allele frequency of the j-th the marker
        Throws:
        java.lang.IllegalArgumentException - if targGT.nMarkers() != map.genPos().size()
        java.lang.IllegalArgumentException - if targGT.nMarkers() != maf.size()
        java.lang.NullPointerException - if (targGT == null || map == null || maf == null)

    • Method Detail

      • nMarkers

        public int nMarkers()
        Returns the number of markers.
        Returns:
        the number of markers

      • nTargSamples

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

      • nIbs2Segments

        public int nIbs2Segments​(int targSample)
        Returns the number of IBS2 segments for the specified target sample
        Parameters:
        targSample - a target sample index
        Returns:
        the number of IBS2 segments for the specified target sample
        Throws:
        java.lang.IndexOutOfBoundsException - if targSample < 0 || targSample >= this.nTargSamples()

      • areIbs2

        public boolean areIbs2​(int targSample,
                       int otherSample,
                       int marker)
        Returns true if (otherSample < this.nTargSamples() and the specified samples are estimated to be IBS2 at the specified marker, and returns false otherwise.
        Parameters:
        targSample - a target sample index
        otherSample - a sample index
        marker - a marker index
        Returns:
        true if the specified samples are estimated to be IBD2 at the specified marker
        Throws:
        java.lang.IndexOutOfBoundsException - if (targSample < 0 || targSample >= this.nTargSamples())
        java.lang.IndexOutOfBoundsException - if otherSample < 0
        java.lang.IndexOutOfBoundsException - if (marker < 0 || marker >= this.nMarkers())

      • areIbs2

        public boolean areIbs2​(int targSample,
                       int otherSample,
                       int start,
                       int inclEnd)
        Returns true if (0 <= otherSample && otherSample < this.nTargSamples()) and the specified samples are estimated to be IBS2 within the specified interval and returns false otherwise.
        Parameters:
        targSample - a target sample index
        otherSample - a sample index
        start - the starting marker index
        inclEnd - the ending marker index (inclusive)
        Returns:
        true if (0 <= otherSample && otherSample < this.nTargSamples()) and the specified samples are estimated to be IBS2 within the specified interval
        Throws:
        java.lang.IndexOutOfBoundsException - if (targSample < 0 || targSample >= this.nTargSamples())
        java.lang.IndexOutOfBoundsException - if start > inclEnd