Package imp

Class ImpData

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

Class ImpData contains the input data for imputation of ungenotyped markers.

Instances of class ImpData are immutable.

  • Constructor Summary

    Constructors
    Constructor
    Description
    ImpData(Par par, Window window, GT phasedTarg, GeneticMap map)
    Constructs a new ImpData instance from the specified data.

  • Method Summary

    Modifier and Type
    Method
    Description
    int
    allele(int cluster, int hap)
    Returns the specified target marker cluter alleles for the reference and target haplotypes.
    float
    errProb(int cluster)
    Returns the probability that the allele carried by the specified target marker cluster matches the allele labeling the latent HMM state.
    IndexArray
    hapToSeq(int cluster)
    Returns the specified target marker cluster alleles for the reference and target haplotypes.
    MarkerIndices
    markerIndices()
     
    int
    nClusters()
    Return the number of target marker clusters.
    int
    nHaps()
    Return the total number of reference and target haplotypes.
    int
    nInputTargHaps()
    Return the number of input target haplotypes.
    int
    nRefHaps()
    Return the number of reference haplotypes.
    int
    nTargHaps()
    Return the number of target haplotypes.
    int
    nTargSamples()
    Returns the number of target samples.
    Par
    par()
    Returns the command line parameters
    double[]
    pos()
    Return an array of size this.nClusters() containing the the genetic map positions of the target marker clusters.
    double
    pos(int cluster)
    Return the genetic map position of the specified target marker cluster.
    float
    pRecomb(int cluster)
    Return the probability of recombination between the specified target marker cluster and the previous target marker cluster.
    int
    refClusterEnd(int cluster)
    Returns the index of the reference marker corresponding to the end (exclusive) of the specified target marker cluster.
    int
    refClusterStart(int cluster)
    Returns the index of the reference marker corresponding to the start (inclusive) of the specified target marker cluster.
    RefGT
    refGT()
    Return the reference genotype data
    int
    targClusterEnd(int cluster)
    Returns the target marker index corresponding to the end (exclusive) of the specified marker cluster.
    int
    targClusterStart(int cluster)
    Returns the target marker index corresponding to the start (inclusive) of the specified marker cluster.
    GT
    targGT()
    Return the phased target genotype data.
    Samples
    targSamples()
    Returns the list of target samples.
    double
    weight(int refMarker)
    Return the weight for the HMM state probability at the preceding target marker cluster when estimating the HMM state probability at the specified reference marker via linear interpolation of HMM state probabilities at the preceding and succeeding target marker clusters.

    Methods inherited from class java.lang.Object

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

  • Constructor Details

  • Method Details

    • par

      public Par par()
      Returns the command line parameters
      Returns:
      the command line parameters

    • markerIndices

      public MarkerIndices markerIndices()

    • refGT

      public RefGT refGT()
      Return the reference genotype data
      Returns:
      the reference genotype data

    • targGT

      public GT targGT()
      Return the phased target genotype data. The isPhased() method of the returned object returns true.
      Returns:
      the phased target genotype data

    • targClusterStart

      public int targClusterStart(int cluster)
      Returns the target marker index corresponding to the start (inclusive) of the specified marker cluster.
      Parameters:
      cluster - index of a target marker cluster
      Returns:
      the target marker index corresponding to the start (inclusive) of the specified marker cluster
      Throws:
      IndexOutOfBoundsException - if cluster < 0 || cluster >= this.nClusters()

    • targClusterEnd

      public int targClusterEnd(int cluster)
      Returns the target marker index corresponding to the end (exclusive) of the specified marker cluster.
      Parameters:
      cluster - index of a target marker cluster
      Returns:
      the target marker index corresponding to the end (exclusive) of the specified marker cluster
      Throws:
      IndexOutOfBoundsException - if cluster < 0 || cluster >= this.nClusters()

    • refClusterStart

      public int refClusterStart(int cluster)
      Returns the index of the reference marker corresponding to the start (inclusive) of the specified target marker cluster.
      Parameters:
      cluster - index of a target marker cluster
      Returns:
      the index of the reference marker corresponding to the start (inclusive) of the specified target marker cluster
      Throws:
      IndexOutOfBoundsException - if cluster < 0 || cluster >= this.nClusters()

    • refClusterEnd

      public int refClusterEnd(int cluster)
      Returns the index of the reference marker corresponding to the end (exclusive) of the specified target marker cluster.
      Parameters:
      cluster - index of a target marker cluster
      Returns:
      the index of the reference marker corresponding to the end (exclusive) of the specified target marker cluster
      Throws:
      IndexOutOfBoundsException - if cluster < 0 || cluster >= this.nClusters()

    • nClusters

      public int nClusters()
      Return the number of target marker clusters.
      Returns:
      the number of target marker clusters

    • targSamples

      public Samples targSamples()
      Returns the list of target samples.
      Returns:
      the list of target samples

    • nTargSamples

      public int nTargSamples()
      Returns the number of target samples.
      Returns:
      the number of target samples

    • nHaps

      public int nHaps()
      Return the total number of reference and target haplotypes.
      Returns:
      the total number of reference and target haplotypes

    • nRefHaps

      public int nRefHaps()
      Return the number of reference haplotypes.
      Returns:
      the number of reference haplotypes

    • nTargHaps

      public int nTargHaps()
      Return the number of target haplotypes.
      Returns:
      the number of target haplotypes

    • nInputTargHaps

      public int nInputTargHaps()
      Return the number of input target haplotypes. Each sample with haploid input data contributes only one haplotype to the total.
      Returns:
      the number of input target haplotypes

    • allele

      public int allele(int cluster, int hap)
      Returns the specified target marker cluter alleles for the reference and target haplotypes. Alleles for the reference haplotypes precede alleles for the target haplotypes. If (this.nRefHaps() <= hap && hap < this.nHaps()) then (this.allele(marker, hap) == this.targAllele(marker, hap - this.nRefHaps())
      Parameters:
      cluster - index of a target marker cluster
      hap - a haplotype index
      Returns:
      the specified target marker cluster allele for the specified haplotype
      Throws:
      IndexOutOfBoundsException - if cluster < 0 || cluster >= this.nClusters()
      IndexOutOfBoundsException - if haplotype < 0 || haplotype >= this.nHaps()

    • hapToSeq

      public IndexArray hapToSeq(int cluster)
      Returns the specified target marker cluster alleles for the reference and target haplotypes. Alleles for the reference haplotypes precede alleles for the target haplotypes. The returned value will satisfy (this.hapToSeq(cluster).get(hap)==this.allele(cluster, hap)) for any cluster and hap satisfying (0 <= cluster && cluster < this.nClusters()) and (0 <= hap && hap < this.nHaps())
      Parameters:
      cluster - index of a target marker cluster
      Returns:
      the specified target marker cluster alleles for the reference and target haplotypes
      Throws:
      IndexOutOfBoundsException - if cluster < 0 || cluster >= this.nClusters()

    • errProb

      public float errProb(int cluster)
      Returns the probability that the allele carried by the specified target marker cluster matches the allele labeling the latent HMM state.
      Parameters:
      cluster - index of a target marker cluster
      Returns:
      the probability that the allele carried by the specified target marker cluster matches the allele labeling the latent HMM state.
      Throws:
      IndexOutOfBoundsException - if cluster < 0 || cluster >= this.nClusters()

    • pos

      public double pos(int cluster)
      Return the genetic map position of the specified target marker cluster.
      Parameters:
      cluster - index of a target marker cluster
      Returns:
      the genetic map position of the specified target marker cluster
      Throws:
      IllegalArgumentException - if cluster < 0 || marker >= this.nClusters()

    • pos

      public double[] pos()
      Return an array of size this.nClusters() containing the the genetic map positions of the target marker clusters.
      Returns:
      the genetic map positions of the target marker clusters

    • pRecomb

      public float pRecomb(int cluster)
      Return the probability of recombination between the specified target marker cluster and the previous target marker cluster. Returns 0 if (cluster == 0).
      Parameters:
      cluster - index of a target marker cluster
      Returns:
      the probability of recombination between the specified target marker cluster and the previous target marker cluster
      Throws:
      IllegalArgumentException - if cluster < 0 || cluster >= this.nClusters()

    • weight

      public double weight(int refMarker)
      Return the weight for the HMM state probability at the preceding target marker cluster when estimating the HMM state probability at the specified reference marker via linear interpolation of HMM state probabilities at the preceding and succeeding target marker clusters.
      Parameters:
      refMarker - a reference marker index
      Returns:
      the weight for the HMM state probability at the preceding target marker cluster when estimating the HMM state probability at the specified reference marker via linear interpolation
      Throws:
      IllegalArgumentException - if refMarker < 0 || refMarker >= this.refGT().nMarkers()