This program finds approximations to the maximum likelihood estimates of
haplotype frequencies from a sample of genotyped individuals.
- input.par is a LINKAGE parameter file
- input.ped is a LINKAGE pedigree file. Only the
genotype data from this file are used, the individuals are
assumed to be unrelated.
- threshold is a minimum value for a haplotype frequency. At each iteration
any haplotype with a lower estimated frequency will be eliminated to save time
and space. The default value is 0.
- max_iterations is an upper bound on the number of iteration performed at
each stage of the algorithm. The default value is infinite, in which case
the algorithm continues to convergence.
Like the program GCHap, the program uses the gene counting method, or EM algorithm,
to iterate between reconstructing the haplotypes and estimating
haplotype frequencies. However, to save time and space haplotypes with
low frequency are eliminated at each stage.
The results are written to the standard output file.
There is a line for each haplotype with a positive frequency MLE,
the frequency is given first in the line followed by the alleles
of the haplotype.
These are followed by two lines for each individual giving the
reconstructed haplotypes, one haplotype on each line.
| Methods inherited from class java.lang.Object |
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
ApproxGCHap
alun.gchap.ApproxGCHap