Compute engine for haplotype EM algorithm
For internal use within the haplo.stats library
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)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 |
|
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? |
For internal use within the haplo.stats library
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