Package sample

Interface Summary

Interface	Description
DiploidStates	Class DiploidStates represents a list of iterators (one iterator for each marker) that iterate over a subset of diploid HMM states at a marker.
SingleBaumInterface	Interface SingleBaumInterface has methods for sampling haplotype pairs.

Class Summary

Class	Description
ConsumeSingleSamples	Class ConsumeSingleSamples samples haplotype pairs conditional on the observed genotype data and a haplotype frequency model.
DuoBaumLevel	Class DuoBaumLevel computes forward and backward Baum values at a level of a hidden Markov model (HMM) whose states are ordered edge trios of a leveled directed acyclic graph (DAG).
DuoNodes	Class DuoNodes stores ordered node trios and associated values.
HapBaumLevel	Class HapBaumLevel computes forward and backward Baum values for a haploid hidden Markov model (HMM) whose states are edges of a leveled directed acyclic graph (DAG).
HaplotypeCoder	Class HaplotypeCoder indexes the observed allele sequences in reference and target haplotype pairs for a list of consecutive markers.
HapNodes	Class HapNodes stores nodes and associated values.
ImputationData	Class ImputationData contains the input data that is required for imputation of ungenotyped markers in the imputation target.
LSHapBaum	Class LSHapBaum implements the Baum hidden Markov model forward and backward algorithms for imputing missing alleles on a target haplotype.
RecombSingleBaum	Class RestrictedSingleBaum implements the Baum forward and backward algorithms for a hidden Markov model (HMM) of an individual's genotype data.
RecombSingleBaumLevel	Class RestrictedSingleBaumLevel computes forward and backward Baum values at a level of a hidden Markov model (HMM) whose states are ordered edge pairs of a leveled directed acyclic graph (DAG).
RecombSingleNodes	Class RecombSingleNodes stores ordered node pairs and associated values.
RefHapSeg	Class RefHapSeg represents a chromosome segment of reference haplotypes.
RefHapSegs	Class RefHapSegs represents reference haplotypes that span segments determined by non-overlapping clusters of markers.
RestrictedDag	Class RestrictedDag is a wrapper for a Dag object that stores segments of identity by descent.
SamplerData	Class SamplerData contains immutable input data for the current marker window.
SingleBaum	Class SingleBaum implements the Baum forward and backward algorithms for a hidden Markov model (HMM) of an individual's genotype data.
SingleBaumLevel	Class SingleBaumLevel computes forward and backward Baum values at a level of a hidden Markov model (HMM) whose states are ordered edge pairs of a leveled directed acyclic graph (DAG).
SingleNodes	Class SingleNodes stores ordered node pairs and associated values.