> On 6 Oct 2016, at 17:51, Bert Gunter <[email protected]> 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 > <[email protected]> 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 >> >> [email protected] >> >> ______________________________________________ >> [email protected] mailing list -- To UNSUBSCRIBE and more, see >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code. -- Federico Calboli Ecological Genetics Research Unit Department of Biosciences PO Box 65 (Biocenter 3, Viikinkaari 1) FIN-00014 University of Helsinki Finland [email protected] ______________________________________________ [email protected] mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
