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haplo.stats (version 1.9.7)

haplo.em.fitter: Compute engine for haplotype EM algorithm

Description

For internal use within the haplo.stats library

Usage

haplo.em.fitter(n.loci, n.subject, weight, geno.vec, n.alleles,
                max.haps, max.iter, loci.insert.order, min.posterior, 
                tol, insert.batch.size, random.start, iseed1, iseed2, 
                iseed3, verbose)

Arguments

n.loci

number of loci in genotype matrix

n.subject

number of subjects in the sample

weight

numeric weights

geno.vec

vectorized genotype matrix

n.alleles

numeric vector giving number of alleles at each marker

max.haps

maximum unique haplotypes in the sample

max.iter

maximum iterations to perform in the fitter

loci.insert.order

order to insert loci for progressive insertion

min.posterior

after insertion and maximization, discard haplotype pairs per person that do not meet minimum posterior prob

tol

convergence tolerance for E-M steps

insert.batch.size

number of markers to insert per batch

random.start

logical; if TRUE, allow for random starting values of haplotype frequencies

iseed1

random seed for algorithm

iseed2

random seed for algorithm

iseed3

random seed for algorithm

verbose

logical, print long, verbose output from E-M steps?

Details

For internal use within the haplo.stats library