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

[Nevil Amos]

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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>>   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
>>
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>> End of R-sig-genetics Digest, Vol 7, Issue 1
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