Class GeneCountAlleles

java.lang.Object
  GeneCountAlleles

public class GeneCountAlleles
extends java.lang.Object

This program calculates maximum likelihood estimates of allele frequencies from genotypes observed in individuals related in pedigrees.

Usage : java GeneCountAlleles input.par input.ped [conv_thresh] [-a]

where

• input.par is the original LINKAGE parameter file.
• input.ped is the original LINKAGE pedigree file.
• conv_thresh is an optional parameter specifiying the largest difference between allele frequencies in successive iterations that is acceptable before convergence is assumed. The default value is 0.000001.
• if -a is specified the frequencies for all loci are estimated (see below).

The output is a linkage parameter file that is the same as the old one, except that the original allele frequencies will be replaced by the new maximum likelihood estimates. This is writen to standard output.

This program is an extension of C A B Smith's gene counting method or EM algorithm. It works by iteratively inferring the genotypes of the founders in a pedigree given the current alleles frequency estimates, the pedigree structure and any genotypes observed in the pedigree (the E step). From the posterior distribution of the founder alleles frequencies new maximum likelihood estimates for the allele frequencies are derived (the M step).

The program also uses C A B Smith's trick of using the rate of convergence of the algorithm to estimate the curvature of the likelihood, and hence get an inflation factor for the variance of the estimators. As the program works through each locus it outputs to the screen the initial estimates, the final estimates, and the standard errors of the estimates incorporating the inflation factor.

In a typical use of this program the input parameter file will contain trait data coded as LINKAGE affection status loci. Because the pedigrees are usually ascertained in ways that bias the estimation of alleles at trait loci the default is not to estimate these frequencies but only those for LINKAGE numbered allele loci. To force estimation at all loci the -a is specified on the command line.

Constructor Summary

GeneCountAlleles()

Method Summary

static void

main(java.lang.String[] args)

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

GeneCountAlleles

public GeneCountAlleles()

Method Detail

main

public static void main(java.lang.String[] args)