haplo.enum {haplo.stats}R Documentation

Enumerate all possible pairs of haplotypes that are consistent with a set of un-phased multilocus markers

Description

Given subject un-phased genotype hmat, enumerate all possible pairs of haplotypes, and return enumerated pairs in matrices h1 and h2.

Usage

haplo.enum(hmat)

Arguments

hmat A genotype vector of length 2*K (K = number of loci). When used in haplo.em, it is a single row of a genotype matrix.

Details

For a pair of haplotypes, if there are H sites that are heterozygous, then there are 2 raised to (H-1) possible pairs to enumerate. To achieve this, the algorithm moves across the loci that are heterozygous (after the 1st heterozygous locus), flipping alleles at heterozygous locations to enumerate all possible pairs of haplotpes, and appending results as rows of the output matrices h1, and h2.

Value

List with components:

h1 A matrix of enumerated haplotypes. If there are N enumerations, h1 will have dimension N x K.
h2 Similar to h1, a matrix of enumerated haplotypes for the second members of the pairs of haplotypes. Haplotype pairs in h1 and h2 match by the same row number.

Side Effects

References

See Also

haplo.em

Examples



[Package Contents]