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

In haplo.stats: Statistical Analysis of Haplotypes with Traits and Covariates when Linkage Phase is Ambiguous

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

haplo.stats documentation built on May 29, 2024, 9:53 a.m.