Class McLinkLD

java.lang.Object
  McLinkLD

public class McLinkLD
extends java.lang.Object

This program calculates linkage statistics while jointly estimating a model for linkage disequilibrium between the loci. It successively updates the LD model given the current haplotypes for the founders in the pedigree, then updates the genotypes and inheritance states of the pedigree given the current LD model and uses these to compute linkage statistics.

Usage java McLink input.par input.ped [n_simulations] [-v/-t]

where

• input.par is a LINKAGE parameter file
• input.ped is a LINKAGE pedigree file
• n_simulations is the number of MCMC samples to use in the calculations. The default is 1000.
• If -v option is specified lod scores are output after each iteration which may be useful in tracking the performance of the sampler. If -t is specified there is no intermediate output. -t is the default.

The output is a row of TLOD, or complex lod score, statistics for each locus. There is a column for each values of the recombination fraction in {0.0, 0.01, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 0.99, 1}.

Constructor Summary

McLinkLD()

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

McLinkLD

public McLinkLD()

Method Detail

main

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