From John.Cole ARS.USDA.GOV Thu Mar 8 06:35:45 2012
From: "Cole, John" <John.ColeARS.USDA.GOV>
Subject: RE: create Pedigree applying DATA and huge PEDIGREE files
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Thu, 08 Mar 2012 06:35:45 -0600
Dear AnGenMapers-
I appreciate Liz Hare's kind endorsement of my pedigree software (PyPedal),
but I just wanted to note that it (currently) stores the entire pedigree in
memory, so if you want to work with huge pedigrees you must have lots of
RAM, and the you will run up against limitations on how much memory your OS
can directly address. While I use the software mostly for working with
smaller pedigrees (e.g., thousands of animals) I ahve used it on a
population of about 600,000 animals.
However, I am like many of the respondents in not really understanding what
exactly the original poster is trying to do. PyPedal can simulate
pedigrees, but it does not simulate an actual selection program, so it may
or may not fit your needs.
Best wishes,
John
--
Dr. John B. Cole, Research Geneticist (Animal)
Animal Improvement Programs Laboratory, ARS, USDA
Room 306, Bldg 005, BARC-West
10300 Baltimore Avenue
Beltsville, MD 20705-2350
E-mail: john.colears.usda.gov Phone: 301-504-8665 Cell: 301-213-7480 Fax:
301-504-8092
________________________________________
> From: David Henderson [dnadavenatorgmail.com]
> Sent: Thursday, March 08, 2012 3:45 AM
> To: Multiple Recipients of <AnGenMapanimalgenome.org>
> Subject: Re: create Pedigree applying DATA and huge PEDIGREE files
>
> Being one of the authors of GeneticsPed (and the one who wrote the C++ code
> that calculates A-inverse), I'm pretty familiar with it's limitations. If
> your data can fit in memory in R, then GeneticsPed might work. The A-
> inverse matrix does use sparse storage and half stores the matrix in the
> C++ part, but when the matrix is passed back into R it is converted to a
> full storage matrix. So, you'll need enough RAM to store both the pedigree
> and an n x n (where n is the total number
> of individuals in the pedigree) matrix of doubles. There used to be a
> version that did sorting, but for various reasons it is not in the
> current version of the package. Thus, you'll need to sort the pedigree
> first. One of the many things I need to fix in the package.
>
> The pedigreemm package sounds like it's pulling its A-inverse matrix from
> C/C++ into a sparse matrix and likely has a better chance of working for
> you.
>
> I have to admit I'm also a bit confused about what you hope to achieve.
>
> Dave H
>
> On Wed, 2012-03-07 at 02:07 -0600, Rodrigo Gularte Mérida wrote:
>
>> Hello, There is a package available through Bioconductor called GeneticsPed
>> that does what you ask for. Here is the website
>> http://bioconductor.org/...csPed.html .
>> However, I agree with Gregor, if you have problems building your pedigree
>> file with Fortran, it is possible that you may have the same problems with
>> R. Have you tried using a shell script with tools such as awk, cut, paste,
>> and sed to prepare the pedigree ?
>>
>> best,
>>
>> ******************************************
>> Rodrigo Gularte Mérida
>> Unit of Animal Genomics
>> GIGA - R -- Université de Liège
>> rodrigo.gularteulg.ac.be
>>
>>
>> On 07 Mar 2012, at 08:13, Gregor GORJANC wrote:
>>
>>> Hi,
>>>
>>> On 7 March 2012 07:49, Mahmood Honarvar wrote:
>>>
>>>> Hello Dear All I'm looking for the R-code [or any package] to create
>>>> Pedigree applying DATA and huge PEDIGREE files for Mixed Model Analysis,
>>>> Including Iterative Queries at determine Generations. I used secateurs
>>>> design by karin mayer but its including problems with Huge data files. With
>>>> all respects: Honarvar
>>>
>>>
>>> I am not sure what exactly you want to do and what you were able to achieve
>>> with Secateurs, but if Fortran program is choking, then any R package will
>>> very likely have the same problems!
>>>
>>> --
>>> With regards!
>>>
>>> ----------------------------------------------------------------------
>>> University of Ljubljana Asst. Prof. Gregor Gorjanc, PhD
>>> Biotechnical Faculty www: http://sites.google.com/...gorgorjanc
>>> Animal Science Department blog: http://ggorjan.blogspot.com
>>> Groblje 3 mail: gregor.gorjanc bf.uni-lj.si
>>> SI-1230 Domzale fax: +386 (0)1 724 10 04
>>> Slovenia, Europe tel: +386 (0)1 320 38 61
>>> ----------------------------------------------------------------------
>>
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