Package imp

Class ImpLSBaum

java.lang.Object
imp.ImpLSBaum
public class ImpLSBaum extends Object

Class ImpLSBaum implements a Baum hidden Markov model forward and backward algorithms for computing HMM state probabilities at genotyped markers using IBS-matched reference haplotypes.

Instances of class ImpLSBaum are not thread-safe.

  • Constructor Details

    • ImpLSBaum

      public ImpLSBaum(ImpData impData, ImpIbs ibsHaps)
      Creates a LSHapBaum instance from the specified data.
      Parameters:
      impData - the input data for genotype imputation
      ibsHaps - the IBS haplotype segments
      Throws:
      NullPointerException - if impData == null || ibsStates == null

  • Method Details

    • impute

      public StateProbs impute(int targHap)

      Returns HMM state probabilities at genotyped markers for the specified target haplotype. States with probabilities that are small and inconsequential are excluded from the returned state probabilities.

      Parameters:
      targHap - a target haplotype index
      Returns:
      HMM state probabilities at genotyped markers for the specified target haplotype
      Throws:
      IndexOutOfBoundsException - if targHap < 0 || hap >= this.impData().nTargHaps()

    • impData

      public ImpData impData()
      Return the input data for genotype imputation
      Returns:
      the input data for genotype imputation