Class DownCodeAlleles

java.lang.Object
  DownCodeAlleles

public class DownCodeAlleles
extends java.lang.Object

This program reduces the number of alleles in the models for the given genetic loci to include only alleles that appear in the pedigree file plus, optionally, one catchall allele to represent the unseen alleles which has frequency equal to the total frequency of the original unseen alleles.

A description of the down coding made is also printed: one line for each locus with the new code number for each of the old alleles in order. A zero indicates that the allele is missing and not included in the downcoded model.

Usage : java DownCodeAlleles input.par input.ped [output.par] [output.ped] [-h/s]

where

• input.par is the original LINKAGE parameter file
• input.ped is the original LINKAGE pedigree file
• output.par is the file where the new down coded parameters will be put. The default is to write to standard output.
• output.ped is the file where the new down coded pedigree data will be put. The default is to write to standard output.
• -h/s these are options to specify the down coding strategy.
  • -h this is the default action which is a "hard" down coding where only the alleles that appear in the pedigree are kept.
  • -s this is a "soft" down coding in which all the alleles that appear in the pedigree are kept, along with one catchall allele to represent the unobserved alleles.

Constructor Summary

DownCodeAlleles()

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

DownCodeAlleles

public DownCodeAlleles()

Method Detail

main

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