ibd

Class IbdBaum

java.lang.Object

ibd.IbdBaum

public class IbdBaum
extends java.lang.Object

Class IbdBaum estimates LOD scores for an IBD versus a non-IBD model, and it estimates LOD scores for an HBD versus a non-HBD model.

Instances of class IbdBaum are immutable.

Constructor Summary

Constructors

Constructor and Description
IbdBaum(Dag dag, GL gl) Creates a new IbdBaum instance from the specified data.

Method Summary

Modifier and Type	Method and Description
Dag	dag() Returns the directed acyclic graph that determines the transition probabilities.
static double	freqLod(int hap, int start, int end, HapPairs hapPairs, Dag dag) Returns the estimated frequency of the haplotype segment on the LOD (-Math.log10) scale.
GL	gl() Returns the HMM emission probabilities.
double	hbdLod(int sample, int start, int end) Returns the homozygosity-by-descent (HBD) LOD score.
double	ibdLod(int sampleA, int sampleB, int start, int end) Returns the identity-by-descent (IBD) LOD score.

Methods inherited from class java.lang.Object

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

Constructor Detail

IbdBaum

public IbdBaum(Dag dag,
               GL gl)

Creates a new IbdBaum instance from the specified data.

Parameters:

dag - the directed acyclic graph that determines the transition probabilities

gl - the HMM emission probabilities

Throws:

java.lang.IllegalArgumentException - if dag.markers().equals(gl.markers()) == false

java.lang.NullPointerException - if dag == null || gl == null

Method Detail

dag

public Dag dag()

Returns the directed acyclic graph that determines the transition probabilities.

Returns:

the directed acyclic graph that determines the transition probabilities

gl

public GL gl()

Returns the HMM emission probabilities.

Returns:

the HMM emission probabilities

hbdLod

public double hbdLod(int sample,
                     int start,
                     int end)

Returns the homozygosity-by-descent (HBD) LOD score.

Parameters:

sample - the sample index

start - the start marker index (inclusive)

end - the end marker index (exclusive)

Returns:

the HBD LOD score

Throws:

java.lang.IndexOutOfBoundsException - if sample < 0 || sample >= this.gl().nSamples()

java.lang.IndexOutOfBoundsException - if start < 0 || start > end || end > this.dag.nMarkers()

ibdLod

public double ibdLod(int sampleA,
                     int sampleB,
                     int start,
                     int end)

Returns the identity-by-descent (IBD) LOD score.

Parameters:

sampleA - the first sample index

sampleB - the second sample index

start - the start marker index (inclusive)

end - the end marker index (exclusive)

Returns:

the IBD LOD score

Throws:

java.lang.IndexOutOfBoundsException - if sampleA < 0 || sampleA >= this.gl().nSamples()

java.lang.IndexOutOfBoundsException - if sampleB < 0 || sampleB >= this.gl().nSamples()

java.lang.IndexOutOfBoundsException - if start < 0 || start > end || end > this.dag.nMarkers()

freqLod

public static double freqLod(int hap,
                             int start,
                             int end,
                             HapPairs hapPairs,
                             Dag dag)

Returns the estimated frequency of the haplotype segment on the LOD (-Math.log10) scale.

Parameters:

hap - a haplotype index

start - the start marker index (inclusive)

end - the end marker index (exclusive)

hapPairs - the list of haplotype pairs

dag - the directed acyclic graph that determines the HMM transition probabilities

Returns:

the estimated frequency of the haplotype segment on the LOD (-Math.log10) scale

Throws:

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

java.lang.IndexOutOfBoundsException - if start < 0 || start > end || end > dag.nMarkers()

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