Linkage Analysis of Pedigrees with Loops

Gerard Tromp tromp at
Fri Jun 30 06:38:03 EST 1995

On 29 Jun 1995, Gregory M. Acland wrote:

> 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?

	The degree of slowdown is proportional, although not linearly, to
the number of untyped individuals in the loops. If all individuals are
typed the slowdown is insignificant. If, on the other hand, a large number
of individuals, especially those where the loops are broken and those
above the loops are untyped, there will be a significant slowing of the
	Having maxloops set at more than the number of loops required 
does not affect the computation time although, I think, it incurs a 
penalty in terms of memory usage (use LINKAGE and FASTLINK on a UNIX 
system and have forgotten the whether or how maxloops affects the size of 
the variable segment.)

[deletia regarding FASTLINK and machine type]

> 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 
> College of Veterinary Medicine
> Cornell University
> Hungerford Hill Rd, Ithaca, New York 14853


Gerard Tromp, Ph.D.
Research Assistant Professor		Vox:	215-955-4487
Department of Biochemistry			215-955-4488 
	and Molecular Biology		Fax:	215-955-5393
Thomas Jefferson University
233 South Tenth Street, Room 328	E-mail:	tromp at
Philadelphia, PA 19107 

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