sample

Class ImputationData

java.lang.Object

sample.ImputationData

public class ImputationData
extends java.lang.Object

Class ImputationData contains the input data that is required for imputation of ungenotyped markers in the imputation target.

Instances of class ImputationData are immutable.

Constructor Summary

Constructors

Constructor and Description
ImputationData(Par par, CurrentData cd, SampleHapPairs targetHapPairs, GeneticMap map) Constructs a new ImputationData instance from the specified data.

Method Summary

Modifier and Type	Method and Description
float	errProb(int marker) Returns the specified allele error probability.
int	nClusters() Return the number of target marker clusters.
float	noErrProb(int marker) Returns (1f - this.errProb(marker)).
float	pRecomb(int marker) Return the probability of recombination between the specified marker and the previous marker, or returns 0 if (marker == 0).
int	refAllele(int marker, int haplotype) Returns the specified reference allele.
SampleHapPairs	refHapPairs() Return the reference haplotype pairs.
RefHapSegs	refHapSegs() Return the reference haplotype segments.
int	targetAllele(int marker, int haplotype) Returns the specified target allele.
Samples	targetSamples() Returns the list of target samples.
SampleHapPairs	targHapPairs() Return the target haplotype pairs.
double	weight(int marker) Return the specified weight.

Methods inherited from class java.lang.Object

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

Constructor Detail

ImputationData

public ImputationData(Par par,
                      CurrentData cd,
                      SampleHapPairs targetHapPairs,
                      GeneticMap map)

Constructs a new ImputationData instance from the specified data.

Parameters:

par - the analysis parameters

cd - the reference haplotype data for the current marker window

targetHapPairs - the target haplotype pairs

map - the genetic map

Throws:

java.lang.IllegalArgumentException - if cd.targetMarkers().equals(targetHapPairs.markers() == false

java.lang.IllegalArgumentException - if cd.targetSamples().equals(targetHapPairs.samples()) == false

java.lang.NullPointerException - if any parameter is null

Method Detail

refHapPairs

public SampleHapPairs refHapPairs()

Return the reference haplotype pairs.

Returns:

the reference haplotype pairs

targHapPairs

public SampleHapPairs targHapPairs()

Return the target haplotype pairs.

Returns:

the target haplotype pairs

refHapSegs

public RefHapSegs refHapSegs()

Return the reference haplotype segments.

Returns:

the reference haplotype segments

nClusters

public int nClusters()

Return the number of target marker clusters.

Returns:

the number of target marker clusters

targetSamples

public Samples targetSamples()

Returns the list of target samples.

Returns:

the list of target samples

refAllele

public int refAllele(int marker,
                     int haplotype)

Returns the specified reference allele.

Parameters:

marker - a marker index

haplotype - a haplotype index

Returns:

the specified reference allele

Throws:

java.lang.IndexOutOfBoundsException - if marker < 0 || marker >= this.nClusters()

java.lang.IndexOutOfBoundsException - if haplotype < 0 || haplotype >= this.refHapPairs().nHaps()

targetAllele

public int targetAllele(int marker,
                        int haplotype)

Returns the specified target allele.

Parameters:

marker - a marker index

haplotype - a haplotype index

Returns:

the specified target allele

Throws:

java.lang.IndexOutOfBoundsException - if marker < 0 || marker >= this.nClusters()

java.lang.IndexOutOfBoundsException - if haplotype < 0 || haplotype >= targ.refHapPairs().nHaps()

errProb

public float errProb(int marker)

Returns the specified allele error probability.

Parameters:

marker - the marker index

Returns:

the specified allele error probability

Throws:

java.lang.IndexOutOfBoundsException - if marker < 0 || marker >= this.nClusters()

noErrProb

public float noErrProb(int marker)

Returns (1f - this.errProb(marker)).

Parameters:

marker - a marker index

Returns:

(1f - this.errProb(marker))

Throws:

java.lang.IndexOutOfBoundsException - if marker < 0 || marker >= this.nClusters()

pRecomb

public float pRecomb(int marker)

Return the probability of recombination between the specified marker and the previous marker, or returns 0 if (marker == 0).

Parameters:

marker - a marker index

Returns:

the specified recombination probability

Throws:

java.lang.IllegalArgumentException - if marker < 0 || marker >= this.refHapPairs().nMarkers()

weight

public double weight(int marker)

Return the specified weight.

Parameters:

marker - a marker index

Returns:

the specified weight

Throws:

java.lang.IllegalArgumentException - if marker < 0 || marker >= this.refHapPairs().nMarkers()