[R-sig-genetics] R-sig-genetics Digest, Vol 7, Issue 1

[Ross]

ah - the rgGRR Galaxy code uses python/weave C code and is limited to
biallelics so easy to estimate alleles shared as 0,1 or 2 -
interesting to see how that will work for microsatellites. Probably
not too hard to write R code to do the calculations but I don't know
of any existing routines..

On Mon, Jun 28, 2010 at 10:04 PM, Nevil Amos <nevil.amos at gmail.com> wrote:
> Thanks for the offer Ross,
>
> I'm looking at 8-18 locus microsat data.  I can undertake the calculations
> easily enough elsewhere,.  However if there was a function out there already
> I would have used it since most of my data manipulation and calculations are
> being handled in R: and it would have made things neater.
>
> Ross wrote:
>>
>> No, but I have a tool in Galaxy based on Abecasis' GRR - his software
>> still available but only as 32bit windows app so very limited in terms
>> of sample and genotype sizes.
>> My app reimplements his algorithm - It estimates mean/sd allele
>> sharing for all pairs, then normalizes those for each pedigree
>> relationship group (parent-child/sibs/unrelated/etc..) and does a nice
>> interactive plot.
>> You'll need at least 5k or 10k ld independent SNPs for reasonable results.
>> It's in the rgenetics tools at http://usegalaxy.org - happy to help if
>> you have any questions on using it.
>>
>> On Mon, Jun 28, 2010 at 8:00 PM,  <r-sig-genetics-request at r-project.org>
>> wrote:
>>
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>>> Today's Topics:
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>>>  1. Calcualtion of pairwise relatedness in R: package?
>>>     (Nevil Amos (Sci))
>>>
>>>
>>> ----------------------------------------------------------------------
>>>
>>> Message: 1
>>> Date: Mon, 28 Jun 2010 03:50:06 +1000
>>> From: "Nevil Amos (Sci)" <nevil.amos at monash.edu>
>>> To: R-sig-genetics at r-project.org
>>> Subject: [R-sig-genetics] Calcualtion of pairwise relatedness in R:
>>>       package?
>>> Message-ID:
>>>       <AANLkTilSVYW5HM9WhqFVOe3s41uHNdd1dijT6lWafLF7 at mail.gmail.com>
>>> Content-Type: text/plain
>>>
>>> Is the calculation of pairwise relateness
>>> eg. Queller and Goodnight 1989 avaiable in any R: package?
>>>
>>> cheers
>>>
>>>
>>>
>>> --
>>> Nevil Amos
>>> Molecular Ecology Research Group
>>> Australian Centre for Biodiversity
>>> Monash University
>>> CLAYTON VIC 3800
>>> Australia
>>>
>>>       [[alternative HTML version deleted]]
>>>
>>>
>>>
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>>> End of R-sig-genetics Digest, Vol 7, Issue 1
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>>
>>
>>
>>
>
>



-- 
Ross Lazarus MBBS MPH
Associate Professor, Harvard Medical School
Director of Bioinformatics, Channing Laboratory
181 Longwood Ave., Boston MA 02115, USA.
Tel: +1 617 505 4850