Documentation for AMAKEDATA 1.4

Amakedata is a program which creates data files for linkage analysis 

               Written by Tero Hiekkalinna (Juntunen)
              (C) 1999-2000 Tero Hiekkalinna (Juntunen)

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1. PURPOISE
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This program is used by Autoscan automaticly, but you can run it by hand as 
well if you like make some data files really easy way.

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2. USAGE
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Launch program by typing amakedata in Unix prompt (Check README.install, how to
compile/install amakedata) and then it will ask following:

>>>Makedata 1.4 (06/17/1999). This program creates data files for linkage
>>>analysis. Maxlocus 60. Made by Tero Hiekkalinna
>>>
>>>How many marker loci?

Answer is number of your markers (do not include disease locus!).

>>>Is this set of markers?
>>>(1) Autosomal
>>>(2) Sexlinked

If you choose 1 you will get:

>>>What is the assumed frequecy of the disease allele?

Type your freq. e.g. 0.001.

>>>How many liability classes?

You always have atleast one liability class and if you type 1 and then you get:

>>>Please enter penetrances for liability class 1.
>>>P(Aff|DD)   P(Aff|D+)   P(Aff|++)

Full dominant model would be: 1.0 1.0 0.0
Resessive would be: 1.0 0.0 0.0

First is both disease alleles, second is one disease allele and last one is no 
disease alleles.

If you have more than one liability class, it will ask those as well. And if you
have sexlinked data it will ask penetrances for males and females.

>>>What is the largest number of alleles at any markers?

If you have 13 alleles (or you largest allele number is 13) type 13. Downfreq
will eliminate missing alleles.

>>>Do you want to specify recombination fraction between markers?
>>>(0=No, 1=Yes, 2=AUTOSCAN option)

Option 0: Choose this if you don't what to specify distances.
Option 1: Choose this if you want to specify distances.
Option 2: This option is only for Autoscan. Autoscan uses this automatically.

And finally you will get this:

>>>Indata.dat created! Run downfreq to eliminate alleles
>>>and calculate correct allele frequences.

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3. WARRANTY
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THIS SOFTWARE COMES WITH ABSOLUTELY NO WARRANTY! USE AT YOUR OWN RISK!


(Doc version 1.4, 12/20/2000)