Package imp

package imp
  • Class
    Description
    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.
    HaplotypeCoder
    Class HaplotypeCoder indexes the observed allele sequences in phased reference and target genotype data in a chromosome interval.
    ImpData
    Class ImpData contains the input data for imputation of ungenotyped markers.
    ImpIbs
    Class ImpIbs identifies haplotypes that share a long IBS segment with a specified haplotype.
    ImpLS
    Class ImpLS computes HMM state probabilities at genotyped markers in the target haplotypes.
    ImpLSBaum
    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.
    ImpStates
    Class ImpStates identifies a list of pseudo-reference haplotypes for a target haplotype.
    ImputedRecBuilder
    Class ImputeRecBuilder contains methods for constructing and printing a VCF record in VCF 4.3 format.
    ImputedVcfWriter
    Class ImputedVcfWriter writes observed and imputed genotypes to a VCF output file.
    RefHapHash
    Class RefHapHash stores a hash code for each haplotype in a sublist of reference haplotypes.
    StateProbs
    Class StateProbs stores a subset of Li and Stephens HMM states and associated probabilities for a target haplotype.
    StateProbsFactory
    Class StateProbsFactory stores HMM state probabilities that that can be used to imputed impute missing HMM state probabilities using linear interpolation.