Class SGS

java.lang.Object
  alun.genapps.AlleleSharing
      SGS

Direct Known Subclasses:

SimSGS

public class SGS
extends AlleleSharing

This program calculates the runs of heterozygous sharing for a set of individuals in a pedigree. 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 largest number of individuals at that locus that can share one alleles. We denote this by S_i.
• The longest run containing the locus for which S_i = n, where n is the number of probands.
• The longest run containing the locus for which S_i >= n-1.
• The longest run containing the locus for which S_i >= n-2.
• The longest run containing the locus for which S_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 S_i = n, S_i >= n-1, etc seen across the whole data set is written to the screen.

Usage : java SGS 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

SGS()

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

SGS

public SGS()

Method Detail

main

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