ibd

Class IbsHapSegments

java.lang.Object

ibd.IbsHapSegments

public final class IbsHapSegments
extends java.lang.Object

Class IbsHapSegments identifies IBS haplotype segments in a list of sample halotype pairs.

Instances of IbsHapSegments are immutable.

Reference: Gusev A, Lowe JK, Stoffel M, Daly MJ, Altshuler D, Breslow JL, Friedman JM, Pe'er I (2008) Whole population, genomewide mapping of hidden relatedness. Genome Research 2009;19(2):318-26.

Constructor Summary

Constructors

Constructor and Description
IbsHapSegments(SampleHapPairs haps, double[] pos, double minLength) Constructs a new IbsHapSegments object from the specified data.
IbsHapSegments(SampleHapPairs haps, int minMarkers) Constructs a new IbsHapSegments object with marker positions defined to be marker indices.

Method Summary

Modifier and Type	Method and Description
java.util.List<HapSegment>	filteredFind(int hap) Returns a list of haplotype segments for other haplotypes that are IBS with the specified haplotype and that have length greater than or equal to this.minIbsLength().
java.util.List<HapSegment>	find(int hap) Returns the list of haplotype segments for other haplotypes that are IBS with the specified haplotype and have length greater than or equal to this.minIbsLength().
SampleHapPairs	haps() Returns the sample haplotype pairs.
double	minIbsLength() Returns the minimum length of an IBS segment.
double[]	pos() Returns an array of non-decreasing marker positions whose j-th element is the position of marker this.haps().marker(j).

Methods inherited from class java.lang.Object

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

Constructor Detail

IbsHapSegments

public IbsHapSegments(SampleHapPairs haps,
                      double[] pos,
                      double minLength)

Constructs a new IbsHapSegments object from the specified data.

Parameters:

haps - the sample haplotype pairs

pos - an array of non-decreasing marker positions whose j-th element is the position of marker haps.marker(j)

minLength - the minimum length of a reported IBS segment

Throws:

java.lang.IllegalArgumentException - if haps.nMarkers() != pos.length

java.lang.IllegalArgumentException - if pos[j] < pos[j-1] for any j satisfing (0 < j && j < pos.length)

java.lang.IllegalArgumentException - if (Double.isNaN(pos[j])==true || Double.isInfinite(pos[j]) == true) for any j satisfying (0 <= j && j < pos.length)

java.lang.IllegalArgumentException - if minLength <= 0.0f

java.lang.NullPointerException - if haps == null || pos == null

IbsHapSegments

public IbsHapSegments(SampleHapPairs haps,
                      int minMarkers)

Constructs a new IbsHapSegments object with marker positions defined to be marker indices.

Parameters:

haps - the sample haplotype pairs

minMarkers - the minimum number of shared markers in a reported IBS segment

Throws:

java.lang.NullPointerException - if haps == null

Method Detail

haps

public SampleHapPairs haps()

Returns the sample haplotype pairs.

Returns:

the sample haplotype pairs

pos

public double[] pos()

Returns an array of non-decreasing marker positions whose j-th element is the position of marker this.haps().marker(j).

Returns:

an array of marker positions

minIbsLength

public double minIbsLength()

Returns the minimum length of an IBS segment.

Returns:

the minimum length of an IBS segment

find

public java.util.List<HapSegment> find(int hap)

Returns the list of haplotype segments for other haplotypes that are IBS with the specified haplotype and have length greater than or equal to this.minIbsLength().

Parameters:

hap - the haplotype index

Returns:

a list of IBS haplotype segments

Throws:

java.lang.IndexOutOfBoundsException - if hap < 0 || hap >= this.haps().nHaps()

filteredFind

public java.util.List<HapSegment> filteredFind(int hap)

Returns a list of haplotype segments for other haplotypes that are IBS with the specified haplotype and that have length greater than or equal to this.minIbsLength(). An IBS segment is permitted (but not required) to be excluded from the returned list if both end-points of the IBD segment are interior points of another IBD segment.

Parameters:

hap - the haplotype index

Returns:

a list of IBS haplotype segments

Throws:

java.lang.IndexOutOfBoundsException - if hap < 0 || hap >= this.haps().nHaps()