Package phase

package phase
  • Class
    Description
    BasicPhaseStates
    Class BasicPhaseStates has methods for constructing a Li and Stephens HMM for a target haplotype or target sample.
    CodedSteps
    Class CodedSteps divides phased genotype data into non-overlapping intervals (the steps), indexes the unique allele sequences in each interval, and stores a map of haplotype index to allele sequence index for each interval.
    EstPhase
    Class EstPhase stores input genotype data and the current estimated phased genotypes for each target sample.
    FixedPhaseData
    Class FixedPhaseData stores immutable data for a marker window.
    FwdPbwtPhaser
    Class FwdPbwtPhaser phases input genotype data and imputes missing alleles using the Positional Burrows-Wheeler Transform (PBWT).
    HmmParamData
    Class HmmParamData generates data for estimating allele mismatch and recombination intensity parameters for a haploid Li and Stephens hidden Markov model.
    HmmStateProbs
    Class HmmStateProbs has a method that returns the reference haplotype and probability associated with each HMM state.
    HmmUpdater
    Class HmmUpdater has static methods for next marker updates of forward and backward HMM values.
    Ibs2
    Class Ibs2 stores IBS2 segments that any target sample shares with another target sample.
    Ibs2Markers
    Class Ibs2Markers stores the markers and intervals that are used to detect IBS2 segments.
    Ibs2Sets
    Class Ibs2Sets partitions markers into steps, and stores the sets of samples whose genotypes are consistent with IBS2 in each step.
    LowFreqPbwtPhaseIbs
    Class LowFreqPbwtPhaseIbs uses the Positional Burrows-Wheeler Transform (PBWT) and rare variants to select IBS haplotypes for each sample for each specified genomic interval.
    LowFreqPhaseIbs
    Class LowFreqPhaseIbs identifies haplotypes that share a long IBS segment or a low frequency variant with a specified haplotype in a specified genomic interval.
    LowFreqPhaseStates
    Class LowFreqPhaseStates has methods for constructing a Li and Stephens HMM for a target haplotype.
    MarkerCluster
    Class MarkerCluster represents a partition of markers into contiguous marker clusters.
    ParamEstimates
    Class ParamEstimates estimates the allele mismatch probability and the recombination intensity for a haploid Li and Stephens hidden Markov model.
    PbwtIbsData
    Class PbwtIbsData contains parameters and data for finding haplotypes that share an IBS segment with a target haplotype.
    PbwtPhaseIbs
    Class PbwtPhaseIBS uses the Positional Burrows-Wheeler Transform (PBWT) to find long IBS haplotypes for each sample that contain a specified small genomic interval.
    PbwtPhaser
    Class PbwtPhaser phases input genotype data and imputes missing alleles using the Positional Burrows-Wheeler Transform (PBWT)
    PbwtRecPhaser
    Class PbwtRecPhaser partially phases and imputes genotypes using the Positional Burrows-Wheeler transform.
    PhaseBaum
    Interface PhaseBaum updates the estimated genotype phase of specified samples.
    PhaseBaum2
    Interface PhaseBaum2 updates the estimated genotype phase of specified samples.
    PhaseData
    Class PhaseData stores the current genotype phase estimates and parameter values.
    PhaseLS
    Class PhaseLS contains static methods for estimated genotypes phase using a haploid Li and Stephens hidden Markov model.
    RevPbwtPhaser
    Class RevPbwtPhaser phases input genotype data and imputes missing alleles using the Positional Burrows-Wheeler Transform (PBWT).
    SamplePhase
    Each instance of class SamplePhase stores an estimated haplotype pair for a sample.
    SamplePhase.ClustType
     
    SampleSeg
    Class SampleSeg represents a segment of genotype data in a sample.
    Stage2Baum
    Class Stage2Baum 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.
    Stage2Haps
    Class Stage2Haps stores phased genotypes.
    SwapRate
    Class SwapRate stores the proportion of unphased heterozygotes whose phase with respect to the previous heteroygote has been reversed.