From johnleewalker at arizona.edu Tue Jan 26 17:17:45 2021 From: johnleewalker at arizona.edu (Walker, John-Lee Sky - (johnleewalker)) Date: Tue, 26 Jan 2021 16:17:45 +0000 Subject: [adegenet-forum] Question About Adegenet Message-ID: Hello, I am using microsatellite data to distinguish individual bats. I have created a genind object with my data. One thing I would like to be able to do is determine when I have matching genotypes, in my case it would be if I have "recaptured" and individual. I am unsure if the package includes a function that makes this possible, or not. I have read the PDF pretty thoroughly and explored the forum archives. I would appreciate any feedback greatly. Kind Regards, John-Lee John-Lee Sky Walker Graduate Research Assistant School of Natural Resources and the Environment The University of Arizona Tucson, AZ 85721 Phone: 805-570-7864 [cid:502636e1-eaef-431d-87aa-fddd45839d45] -------------- next part -------------- An HTML attachment was scrubbed... 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Name: Outlook-ogmrddvg.png Type: image/png Size: 5595 bytes Desc: Outlook-ogmrddvg.png URL: From thibautjombart at gmail.com Wed Jan 27 16:42:45 2021 From: thibautjombart at gmail.com (Thibaut Jombart) Date: Wed, 27 Jan 2021 16:42:45 +0100 Subject: [adegenet-forum] Question About Adegenet In-Reply-To: References: Message-ID: Dear John-Lee I think the poppr package has what you need - see "mlg" and related functions at (working on genind objects): https://cran.r-project.org/web/packages/poppr/vignettes/poppr_manual.html#mlg Best Thibaut -- Dr Thibaut Jombart Associate Professor in Outbreak Analytics, London School of Hygiene and Tropical Medicine Senior Lecturer in Genetic Analysis, Imperial College London UK Public Health Rapid Support Team President of RECON: repidemicsconsortium.org https://thibautjombart.netlify.com Twitter: @TeebzR On Wed, 27 Jan 2021 at 10:53, Walker, John-Lee Sky - (johnleewalker) < johnleewalker at arizona.edu> wrote: > Hello, > > I am using microsatellite data to distinguish individual bats. I have > created a genind object with my data. One thing I would like to be able to > do is determine when I have matching genotypes, in my case it would be if I > have "recaptured" and individual. I am unsure if the package includes a > function that makes this possible, or not. I have read the PDF pretty > thoroughly and explored the forum archives. I would appreciate any feedback > greatly. > > Kind Regards, > John-Lee > > John-Lee Sky Walker > Graduate Research Assistant > School of Natural Resources and the Environment > The University of Arizona > Tucson, AZ 85721 > Phone: 805-570-7864 > > > > > _______________________________________________ > adegenet-forum mailing list > adegenet-forum at lists.r-forge.r-project.org > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Outlook-ogmrddvg.png Type: image/png Size: 5595 bytes Desc: not available URL: From zkamvar at gmail.com Wed Jan 27 17:29:28 2021 From: zkamvar at gmail.com (Zhian N. Kamvar) Date: Wed, 27 Jan 2021 08:29:28 -0800 Subject: [adegenet-forum] adegenet-forum Digest, Vol 143, Issue 1 In-Reply-To: References: Message-ID: Hello, You can use the package {poppr} for this purpose as it works quite well with adegenet. In particular, you might be interested in the "clone correction" feature that will remove duplicates from your analysis: https://grunwaldlab.github.io/poppr/articles/mlg.html#clone-correction-1 Hope that helps, Zhian On 1/27/21 3:00 AM, adegenet-forum-request at lists.r-forge.r-project.org wrote: > Send adegenet-forum mailing list submissions to > adegenet-forum at lists.r-forge.r-project.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum > > or, via email, send a message with subject or body 'help' to > adegenet-forum-request at lists.r-forge.r-project.org > > You can reach the person managing the list at > adegenet-forum-owner at lists.r-forge.r-project.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of adegenet-forum digest..." > > > Today's Topics: > > 1. Question About Adegenet (Walker, John-Lee Sky - (johnleewalker)) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 26 Jan 2021 16:17:45 +0000 > From: "Walker, John-Lee Sky - (johnleewalker)" > > To: "adegenet-forum at lists.r-forge.r-project.org" > > Subject: [adegenet-forum] Question About Adegenet > Message-ID: > > > Content-Type: text/plain; charset="iso-8859-1" > > Hello, > > I am using microsatellite data to distinguish individual bats. I have created a genind object with my data. One thing I would like to be able to do is determine when I have matching genotypes, in my case it would be if I have "recaptured" and individual. I am unsure if the package includes a function that makes this possible, or not. I have read the PDF pretty thoroughly and explored the forum archives. I would appreciate any feedback greatly. > > Kind Regards, > John-Lee > > John-Lee Sky Walker > Graduate Research Assistant > School of Natural Resources and the Environment > The University of Arizona > Tucson, AZ 85721 > Phone: 805-570-7864 > > [cid:502636e1-eaef-431d-87aa-fddd45839d45] > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: Outlook-ogmrddvg.png > Type: image/png > Size: 5595 bytes > Desc: Outlook-ogmrddvg.png > URL: > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > adegenet-forum mailing list > adegenet-forum at lists.r-forge.r-project.org > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum > > ------------------------------ > > End of adegenet-forum Digest, Vol 143, Issue 1 > **********************************************