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 and Description |
---|
ImputationData(Par par,
CurrentData cd,
SampleHapPairs targetHapPairs,
GeneticMap map)
Constructs a new
ImputationData instance from the specified data. |
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.
|
public ImputationData(Par par, CurrentData cd, SampleHapPairs targetHapPairs, GeneticMap map)
ImputationData
instance from the specified data.par
- the analysis parameterscd
- the reference haplotype data for the current marker windowtargetHapPairs
- the target haplotype pairsmap
- the genetic mapjava.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
public SampleHapPairs refHapPairs()
public SampleHapPairs targHapPairs()
public RefHapSegs refHapSegs()
public int nClusters()
public Samples targetSamples()
public int refAllele(int marker, int haplotype)
marker
- a marker indexhaplotype
- a haplotype indexjava.lang.IndexOutOfBoundsException
- if
marker < 0 || marker >= this.nClusters()
java.lang.IndexOutOfBoundsException
- if
haplotype < 0 || haplotype >= this.refHapPairs().nHaps()
public int targetAllele(int marker, int haplotype)
marker
- a marker indexhaplotype
- a haplotype indexjava.lang.IndexOutOfBoundsException
- if
marker < 0 || marker >= this.nClusters()
java.lang.IndexOutOfBoundsException
- if
haplotype < 0 || haplotype >= targ.refHapPairs().nHaps()
public float errProb(int marker)
marker
- the marker indexjava.lang.IndexOutOfBoundsException
- if
marker < 0 || marker >= this.nClusters()
public float noErrProb(int marker)
(1f - this.errProb(marker))
.marker
- a marker index(1f - this.errProb(marker))
java.lang.IndexOutOfBoundsException
- if
marker < 0 || marker >= this.nClusters()
public float pRecomb(int marker)
0
if (marker == 0)
.marker
- a marker indexjava.lang.IllegalArgumentException
- if
marker < 0 || marker >= this.refHapPairs().nMarkers()
public double weight(int marker)
marker
- a marker indexjava.lang.IllegalArgumentException
- if
marker < 0 || marker >= this.refHapPairs().nMarkers()