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

Federico Calboli federico.calboli at helsinki.fi
Thu Oct 6 14:56:23 CEST 2016

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


Federico Calboli
Ecological Genetics Research Unit
Department of Biosciences
PO Box 65 (Biocenter 3, Viikinkaari 1)
FIN-00014 University of Helsinki

federico.calboli at helsinki.fi

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