Linkage Analysis of Pedigrees with Loops

Gregory M. Acland gma2 at CORNELL.EDU
Thu Jun 29 20:03:21 EST 1995


I would appreciate advice from anyone with insight or experience into
analysing pedigrees with multiple loops. I understand, from discussions at
Dr Ott's introductory course on Linkage Analysis, that the Linkage package
can be recompiled with the Maxloops constant set at a desired number other
than the default.

How severe are the trade offs?

The pedigrees involved are canine, and do not have huge numbers of
individuals. Probably somewhere in the order of 30 to 50 individuals per
family. The loops are unavoidable, however, as they are prexisting rather
than planned pedigrees. Something like 6 to 10 loops per pedigree is
typical.

Does changing Maxloops to something like 10 increase the compute time
drastically for pedigrees of this sort of size?

I am currently running the Linkage package on a DOS machine (100 Mhz 486,
16 MB RAM), and don't have ready access to a Unix system.

What source programs do I need to compile to yield a version of the Linkage
package customized to deal with this many loops. What are the current
versions that should be used? Is Borland Turbo/Pascal still the compiler of
choice? Are there other compile options that should be considered at the
same time?

Alternatively, can Fastlink deal with loops at all, and if so, can it deal
with this many loops.  If so, can I obtain a DOS-executable version with
the capacity to handle this many loops?

Gregory M. Acland        	       	       	       	       	  (607) 256-5684
[phone]
Center for Canine Genetics & Reproduction       	  (607) 256-5689 [fax]
James A. Baker Institute for Animal Health      	   gma2 at cornell.edu
College of Veterinary Medicine
Cornell University
Hungerford Hill Rd, Ithaca, New York 14853





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