[R] replicating PLINK's --genome calculations.

[Federico Calboli]

> On 6 Oct 2016, at 17:51, Bert Gunter <bgunter.4567 at gmail.com> wrote:
> 
> You may get an answer here, but the Bioconductor site/list is almost
> certainly a better place to post this.

Good call — I would have never though of checking BioC.  In fact the package SNPRelate seems to do what I need.

Best

F



> 
> Cheers,
> Bert
> 
> 
> Bert Gunter
> 
> "The trouble with having an open mind is that people keep coming along
> and sticking things into it."
> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
> 
> 
> On Thu, Oct 6, 2016 at 5:56 AM, Federico Calboli
> <federico.calboli at helsinki.fi> wrote:
>> Hi All,
>> 
>> I have some genetic data and I want to resample it changing the number of individuals and/or the number of markers to show the effects of smaller sample sizes on the pairwise-IBD calculations.  The “standard” I need to follow is PLINK, specifically the --genome option.  I could create multiple subsets of the data, export it an have PLINK do the needed calculations, and then reimport the results in R, but this is obviously pretty silly, especially because it would require creating, exporting and importing a few hundreds files.  I could write the needed functions to do what PLINK does, but I’d rather not reinvent the wheel so it might be worth asking:  is there any package/function that would do (in R) what PLINK does with --genome?
>> 
>> Bets wishes
>> 
>> F
>> 
>> --
>> Federico Calboli
>> Ecological Genetics Research Unit
>> Department of Biosciences
>> PO Box 65 (Biocenter 3, Viikinkaari 1)
>> FIN-00014 University of Helsinki
>> Finland
>> 
>> federico.calboli at helsinki.fi
>> 
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--
Federico Calboli
Ecological Genetics Research Unit
Department of Biosciences
PO Box 65 (Biocenter 3, Viikinkaari 1)
FIN-00014 University of Helsinki
Finland

federico.calboli at helsinki.fi