Class HGS

java.lang.Object
  alun.genapps.AlleleSharing
      HGS

Direct Known Subclasses:

SimHGS

public class HGS
extends AlleleSharing

This program calculates the runs of loci at which the selected individuals are all homozygous, but not necessarily for the same allele. The individuals to consider are specified by having a 1 in the proband field of the input LINKAGE pedigree file. The MakeProbands program can be used to set this field.

The output is a table with 1 line for each locus in the input LINKAGE parameter file. On each line appear

• The name of the locus
• The number of individuals at that locus who are not heterozygous. We denote this by H_i.
• The longest run containing the locus for which H_i = n, where n is the number of probands.
• The longest run containing the locus for which H_i >= n-1.
• The longest run containing the locus for which H_i >= n-2.
• The longest run containing the locus for which H_i >= n-3.

Note that this format choice means that a run of length r will appear r times in the output: once for each locus in the run. This should be taken into account in any estimates of the run length distribution. Alternatively use the -r option below to list each run only once.

The largest runs for which H_i = n, H_i >= n-1, etc seen across the whole data set is written to the screen.

Usage : java HGS input.par input.ped [-r]

where

• input.par is the input LINKAGE parameter file.
• input.ped is the input LINKAGE pedigree file.
• -r if this optional parameter is specified the lengths of the runs where H_i = n are output, as required to estimate the distribution of run lengths

Constructor Summary

HGS()

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

HGS

public HGS()

Method Detail

main

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