Class IntervalLD

java.lang.Object
  alun.util.Main
      IntervalLD

public class IntervalLD
extends Main

This program estimates a interval graphed graphical model for linkage disequilibrium between genetic loci. The data is input in the form of LINKAGE parameter and pedigree files. Even if individuals are related, the relationships will be ignored in the estimation and the sample treated as independent. Missing data will slow the program down considerably, so it would be best to remove unobserved ancestors from the input.

The output is in a format that can be input directly to GeneDrop , SimSGS , and SimHGS .

The graphical model estimated is constrained to have an interval graph, with restrictions on the length of the intervals, and consequently on the extent of possible linkage disequilibrium. By optimizing over a walking window of 100 loci, the program can operate in time linear in the number of loci, and has been used on over 100,000 loci. Two scans are made, one using the Metropolis method so sample states, and the other using random uphill search to optimize the penalized log likelihood.

To estimate general graphical models for linkage disequilirbium use HapGraph .

Usage : java IntervalLD input.par input.ped [window_width] [phase_updates] [metro_sweeps]

where

• input.par is the input LINKAGE parameter file.
• input.ped is the input LINKAGE pedigree file.
• window_width is an optional parameter specifying the number of loci to include in each walking window. The default is 100.
• phase_updates is an optional parameter specifying the number of times the phases are estimated in each window. The default is 5.
• graph_sweeps is an optional parameter specifying the number of sweeps of random graph updates are made in each window before each phase_updates The defult is 5.

Constructor Summary

IntervalLD()

Method Summary

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

Methods inherited from class alun.util.Main

strip

Methods inherited from class java.lang.Object

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

Constructor Detail

IntervalLD

public IntervalLD()

Method Detail

usage

public static void usage()

main

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