Class SimSGS

java.lang.Object
  alun.genapps.AlleleSharing
      SGS
          SimSGS

public class SimSGS
extends SGS

This program performs multi locus gene drop simulations in order to assess the distribution of the length of heterozygously shared genomic regions, as calculated by SGS . The input for SimSGS should be exactly the same as that for SGS.

The output is a table of maximum run lengths. There is one row for each simulation, and on each row are the maximum run length over the given markers for where the number of sharing individuals, S_i, is equal to n, the number of probands, followed by the maximum run length where S_i >= n-1, n-2, and n-3.

Usage : java SimSGS input.par input.ped [n] [ldmodel]

where

• input.par is the input LINKAGE parameter file.
• input.ped is the input LINKAGE pedigree file.
• n_sims an optional parameter specifying the number of simulations to do. The default is 1000.
• ldmodel n optional parameter giving the name of a file with a graphical model for linkage disequilibrium from which to generate the founder haplotypes. See GeneDrop for more information.

Constructor Summary

SimSGS()

Method Summary

static void

main(java.lang.String[] args)

Methods inherited from class alun.genapps.AlleleSharing

hetSharing, homozygotes, homSharing, max, runs

Methods inherited from class java.lang.Object

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

Constructor Detail

SimSGS

public SimSGS()

Method Detail

main

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