From cmaltec ncsu.edu Wed Mar 7 09:59:27 2012
Subject: Re: create Pedigree applying DATA and huge PEDIGREE files
From: Christian Maltecca <cmaltecncsu.edu>
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Wed, 07 Mar 2012 09:59:27 -0600
Hi
The package "pedigree" in R (you can find it on the cran repository) will
allow you to do most of what you are asking but you will likely get a stack
overflow message if your pedigree is 500K
As others pointed out in most cases interpreted languages will hit the wall
before "low level" languages.
If your problem is related to ordering slicing or pruning very large pedigree
files before obtaining A or A^-1 in R very large data can be manipulated
with "relative" ease using for example the package ff (again cran) yet you
will need to do some of your own coding.
Christian
On Wed, Mar 7, 2012 at 10:06 AM, Liz Hare <doggeneearthlink.netwrote:
Depending on exactly what you need to do with this large pedigree, you
might want to try PyPedal: http://pypedal.sourceforge.net/ It will
calculate lots of statistics about the pedigree and can calculate and
invert the A matrix.
Liz
Liz Hare PhD
Dog Genetics LLC
doggeneearthlink.net
http://www.doggenetics.com
--
------------------------------------
Christian Maltecca
Department of Animal Science
North Carolina State University
Campus Box 7621
Raleigh, NC 27695
Office: (919) 515-0812
Fax (919) 515-6884
email: christian_malteccancsu.edu
_
_( }
-= _ << \
`.\__/`/\\
-= '--'\\ `
-= //
\)
|
