Package phase
Class ImputeBaum
- java.lang.Object
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- phase.ImputeBaum
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public class ImputeBaum extends java.lang.Object
Class
ImputeBaum
applies the forward and backward algorithms for a haploid Li and Stephens hidden Markov model at high-frequency markers, and imputes missing genotypes and heterozygote phase at low-frequency markers.Instances of class
ImputeBaum
are not thread-safe.
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Constructor Summary
Constructors Constructor Description ImputeBaum(PhaseIbs phaseIbs, HapImputer hapImputer)
Creates aImputeBaum
instance from the specified data.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description int
nTargSamples()
Returns the number of target samples.void
phase(int sample)
Estimates phased haplotypes for the specified sample.
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Constructor Detail
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ImputeBaum
public ImputeBaum(PhaseIbs phaseIbs, HapImputer hapImputer)
Creates aImputeBaum
instance from the specified data.- Parameters:
phaseIbs
- the IBS haplotypeshapImputer
- an object for imputing haplotypes at low-frequency markers- Throws:
java.lang.NullPointerException
- ifphaseIbs == null || hapImputer == null
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Method Detail
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nTargSamples
public int nTargSamples()
Returns the number of target samples.- Returns:
- the number of target samples
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phase
public void phase(int sample)
Estimates phased haplotypes for the specified sample.- Parameters:
sample
- a sample index- Throws:
java.lang.IndexOutOfBoundsException
- ifsample < 0 || sample >= this.nTargSamples()
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