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

Bert Gunter bgunter.4567 at gmail.com
Thu Oct 6 16:51:29 CEST 2016

You may get an answer here, but the Bioconductor site/list is almost
certainly a better place to post this.


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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