From massimiliano.virgilio at africamuseum.be Tue Jan 6 16:15:01 2015 From: massimiliano.virgilio at africamuseum.be (Virgilio Massimiliano) Date: Tue, 6 Jan 2015 15:15:01 +0000 Subject: [adegenet-forum] individual geographic distances vs population geographic distances Message-ID: Hi and happy new year everybody! I?m trying to perform a Mantel?s test on populations rather than individuals: - I converted my genind data to a genepop object (genind2genpop) - I could calculate genetic distances among populations (dist.genpop) BUT I cannot calculate geographic distances among populations (as I only have individual coordinates in the $other$xy slot of my genuine/genepop object) any suggestion? many thanks in advance Massi -------------- next part -------------- An HTML attachment was scrubbed... URL: From t.jombart at imperial.ac.uk Tue Jan 6 16:20:36 2015 From: t.jombart at imperial.ac.uk (Jombart, Thibaut) Date: Tue, 6 Jan 2015 15:20:36 +0000 Subject: [adegenet-forum] individual geographic distances vs population geographic distances In-Reply-To: References: Message-ID: <2CB2DA8E426F3541AB1907F98ABA6570ABEB6C0D@icexch-m1.ic.ac.uk> Hi there, it has been discussed on this forum recently. Check "process.other" in ?genind2genpop: it will allow you to define the xy coords of your populations as the mean of the individual coordinates. Cheers Thibaut ________________________________ From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Virgilio Massimiliano [massimiliano.virgilio at africamuseum.be] Sent: 06 January 2015 15:15 To: adegenet-forum at lists.r-forge.r-project.org Subject: [adegenet-forum] individual geographic distances vs population geographic distances Hi and happy new year everybody! I?m trying to perform a Mantel?s test on populations rather than individuals: - I converted my genind data to a genepop object (genind2genpop) - I could calculate genetic distances among populations (dist.genpop) BUT I cannot calculate geographic distances among populations (as I only have individual coordinates in the $other$xy slot of my genuine/genepop object) any suggestion? many thanks in advance Massi -------------- next part -------------- An HTML attachment was scrubbed... URL: From massimiliano.virgilio at africamuseum.be Tue Jan 6 16:29:21 2015 From: massimiliano.virgilio at africamuseum.be (Virgilio Massimiliano) Date: Tue, 6 Jan 2015 15:29:21 +0000 Subject: [adegenet-forum] still on Mantel's test Message-ID: Hi again, and happy new year again :-) The second question I have for today is the following: I got this beautiful kernel density of individual geographic vs genetic distances (still playing around with Mantel?s test). It looks like there are a couple of red areas possibly indicating discontinuities between two groups of individuals. Is there a way I can have synthetic information on these two groups or I would just get a list of thousands of inter-individual distances? Cheers Massi -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Rplot.pdf.zip Type: application/zip Size: 4101462 bytes Desc: Rplot.pdf.zip URL: From t.jombart at imperial.ac.uk Tue Jan 6 16:54:06 2015 From: t.jombart at imperial.ac.uk (Jombart, Thibaut) Date: Tue, 6 Jan 2015 15:54:06 +0000 Subject: [adegenet-forum] still on Mantel's test In-Reply-To: References: Message-ID: <2CB2DA8E426F3541AB1907F98ABA6570ABEB6C48@icexch-m1.ic.ac.uk> Hi, and yes, happy new year. Please do not post attachments that large - saved a png your figure would be a lot smaller, with the same quality. I can't really see any clear-cut discontinuity here, though there are some hotspots. However, note that these are pairwise distances (each individual corresponds to several points), so there is not clear interpretation of a group of points in the IBD plot in terms of genetic clusters. What you could merely conclude from discontinuity is that the genetic diversity is structured in geographic patches. Methods exist to define these, but not a simple IBD plot. Cheers Thibaut ________________________________ From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Virgilio Massimiliano [massimiliano.virgilio at africamuseum.be] Sent: 06 January 2015 15:29 To: adegenet-forum at lists.r-forge.r-project.org Subject: [adegenet-forum] still on Mantel's test Hi again, and happy new year again :-) The second question I have for today is the following: I got this beautiful kernel density of individual geographic vs genetic distances (still playing around with Mantel?s test). It looks like there are a couple of red areas possibly indicating discontinuities between two groups of individuals. Is there a way I can have synthetic information on these two groups or I would just get a list of thousands of inter-individual distances? Cheers Massi -------------- next part -------------- An HTML attachment was scrubbed... URL: From massimiliano.virgilio at africamuseum.be Tue Jan 6 16:58:29 2015 From: massimiliano.virgilio at africamuseum.be (Virgilio Massimiliano) Date: Tue, 6 Jan 2015 15:58:29 +0000 Subject: [adegenet-forum] still on Mantel's test In-Reply-To: <2CB2DA8E426F3541AB1907F98ABA6570ABEB6C48@icexch-m1.ic.ac.uk> References: <2CB2DA8E426F3541AB1907F98ABA6570ABEB6C48@icexch-m1.ic.ac.uk> Message-ID: Many thanks for the quick reply, it?s done now All the best M. From: , Thibaut > Date: Tuesday 6 January 2015 16:54 To: Massimiliano Virgilio >, "adegenet-forum at lists.r-forge.r-project.org" > Subject: RE: still on Mantel's test Hi, and yes, happy new year. Please do not post attachments that large - saved a png your figure would be a lot smaller, with the same quality. I can't really see any clear-cut discontinuity here, though there are some hotspots. However, note that these are pairwise distances (each individual corresponds to several points), so there is not clear interpretation of a group of points in the IBD plot in terms of genetic clusters. What you could merely conclude from discontinuity is that the genetic diversity is structured in geographic patches. Methods exist to define these, but not a simple IBD plot. Cheers Thibaut ________________________________ From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Virgilio Massimiliano [massimiliano.virgilio at africamuseum.be] Sent: 06 January 2015 15:29 To: adegenet-forum at lists.r-forge.r-project.org Subject: [adegenet-forum] still on Mantel's test Hi again, and happy new year again :-) The second question I have for today is the following: I got this beautiful kernel density of individual geographic vs genetic distances (still playing around with Mantel?s test). It looks like there are a couple of red areas possibly indicating discontinuities between two groups of individuals. Is there a way I can have synthetic information on these two groups or I would just get a list of thousands of inter-individual distances? Cheers Massi -------------- next part -------------- An HTML attachment was scrubbed... URL: From massimiliano.virgilio at africamuseum.be Wed Jan 7 20:46:16 2015 From: massimiliano.virgilio at africamuseum.be (Virgilio Massimiliano) Date: Wed, 7 Jan 2015 19:46:16 +0000 Subject: [adegenet-forum] adegenet-forum Digest, Vol 77, Issue 2 In-Reply-To: References: Message-ID: <2904A1C6-AFB1-4128-A403-900C29957B94@africamuseum.be> many thanks again Thibaut :-) all the best M. __________________________________ Massimiliano Virgilio, PhD Royal Museum for Central Africa Leuvensesteenweg 13, B-3080 Tervuren, Belgium, +32 (0) 27695366 massimiliano.virgilio at africamuseum.be http://www.africamuseum.be/home/contact/staff/VIRGILIO_Massimiliano/ On 07 Jan 2015, at 12:00, 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. Re: still on Mantel's test (Jombart, Thibaut) 2. Re: still on Mantel's test (Virgilio Massimiliano) ---------------------------------------------------------------------- Message: 1 Date: Tue, 6 Jan 2015 15:54:06 +0000 From: "Jombart, Thibaut" To: Virgilio Massimiliano , "adegenet-forum at lists.r-forge.r-project.org" Subject: Re: [adegenet-forum] still on Mantel's test Message-ID: <2CB2DA8E426F3541AB1907F98ABA6570ABEB6C48 at icexch-m1.ic.ac.uk> Content-Type: text/plain; charset="windows-1252" Hi, and yes, happy new year. Please do not post attachments that large - saved a png your figure would be a lot smaller, with the same quality. I can't really see any clear-cut discontinuity here, though there are some hotspots. However, note that these are pairwise distances (each individual corresponds to several points), so there is not clear interpretation of a group of points in the IBD plot in terms of genetic clusters. What you could merely conclude from discontinuity is that the genetic diversity is structured in geographic patches. Methods exist to define these, but not a simple IBD plot. Cheers Thibaut ________________________________ From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Virgilio Massimiliano [massimiliano.virgilio at africamuseum.be] Sent: 06 January 2015 15:29 To: adegenet-forum at lists.r-forge.r-project.org Subject: [adegenet-forum] still on Mantel's test Hi again, and happy new year again :-) The second question I have for today is the following: I got this beautiful kernel density of individual geographic vs genetic distances (still playing around with Mantel?s test). It looks like there are a couple of red areas possibly indicating discontinuities between two groups of individuals. Is there a way I can have synthetic information on these two groups or I would just get a list of thousands of inter-individual distances? Cheers Massi -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Message: 2 Date: Tue, 6 Jan 2015 15:58:29 +0000 From: Virgilio Massimiliano To: "Jombart, Thibaut" , "adegenet-forum at lists.r-forge.r-project.org" Subject: Re: [adegenet-forum] still on Mantel's test Message-ID: Content-Type: text/plain; charset="windows-1252" Many thanks for the quick reply, it?s done now All the best M. From: , Thibaut > Date: Tuesday 6 January 2015 16:54 To: Massimiliano Virgilio >, "adegenet-forum at lists.r-forge.r-project.org" > Subject: RE: still on Mantel's test Hi, and yes, happy new year. Please do not post attachments that large - saved a png your figure would be a lot smaller, with the same quality. I can't really see any clear-cut discontinuity here, though there are some hotspots. However, note that these are pairwise distances (each individual corresponds to several points), so there is not clear interpretation of a group of points in the IBD plot in terms of genetic clusters. What you could merely conclude from discontinuity is that the genetic diversity is structured in geographic patches. Methods exist to define these, but not a simple IBD plot. Cheers Thibaut ________________________________ From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Virgilio Massimiliano [massimiliano.virgilio at africamuseum.be] Sent: 06 January 2015 15:29 To: adegenet-forum at lists.r-forge.r-project.org Subject: [adegenet-forum] still on Mantel's test Hi again, and happy new year again :-) The second question I have for today is the following: I got this beautiful kernel density of individual geographic vs genetic distances (still playing around with Mantel?s test). It looks like there are a couple of red areas possibly indicating discontinuities between two groups of individuals. Is there a way I can have synthetic information on these two groups or I would just get a list of thousands of inter-individual distances? Cheers Massi -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ _______________________________________________ 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 77, Issue 2 ********************************************* -------------- next part -------------- An HTML attachment was scrubbed... URL: From yan.hou at nhm.uio.no Mon Jan 12 22:26:04 2015 From: yan.hou at nhm.uio.no (Yan Hou) Date: Mon, 12 Jan 2015 22:26:04 +0100 Subject: [adegenet-forum] glPlot: which sample is used as the reference? Message-ID: <54B43BEC.3020202@nhm.uio.no> Hi, I managed to use glPlot( SNPs,posi="topleft" ) to present the position of SNPs in my concatenated and aligned RAD-seq data matrix. When looking at the figure, I wonder which sample was used as the reference? The first sample in the input file or the sample with most complete sequence data? My first sample has a large number of missing data, so I wonder? Cheers, Yan -------------- next part -------------- An HTML attachment was scrubbed... URL: From t.jombart at imperial.ac.uk Tue Jan 13 18:58:18 2015 From: t.jombart at imperial.ac.uk (Jombart, Thibaut) Date: Tue, 13 Jan 2015 17:58:18 +0000 Subject: [adegenet-forum] glPlot: which sample is used as the reference? In-Reply-To: <54B43BEC.3020202@nhm.uio.no> References: <54B43BEC.3020202@nhm.uio.no> Message-ID: <2CB2DA8E426F3541AB1907F98ABA6570ABEBD849@icexch-m1.ic.ac.uk> Hi there, individuals are plotted according to their order in the genlight object (individuals' indices are indicated on the y-axis. Cheers Thibaut ________________________________ From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Yan Hou [yan.hou at nhm.uio.no] Sent: 12 January 2015 21:26 To: adegenet-forum at lists.r-forge.r-project.org Cc: Yan Hou Subject: [adegenet-forum] glPlot: which sample is used as the reference? Hi, I managed to use glPlot( SNPs,posi="topleft" ) to present the position of SNPs in my concatenated and aligned RAD-seq data matrix. When looking at the figure, I wonder which sample was used as the reference? The first sample in the input file or the sample with most complete sequence data? My first sample has a large number of missing data, so I wonder? Cheers, Yan -------------- next part -------------- An HTML attachment was scrubbed... URL: From t.jombart at imperial.ac.uk Thu Jan 15 16:42:41 2015 From: t.jombart at imperial.ac.uk (Jombart, Thibaut) Date: Thu, 15 Jan 2015 15:42:41 +0000 Subject: [adegenet-forum] glPlot: which sample is used as the reference? In-Reply-To: <54B571AF.5010300@nhm.uio.no> References: <54B43BEC.3020202@nhm.uio.no> <2CB2DA8E426F3541AB1907F98ABA6570ABEBD849@icexch-m1.ic.ac.uk>, <54B571AF.5010300@nhm.uio.no> Message-ID: <2CB2DA8E426F3541AB1907F98ABA6570ABEBDC28@icexch-m1.ic.ac.uk> Hi there, I suspected this misunderstanding. genlight stores biallelic data are coded as binary, so the first allele is 0 and the second is 1 for all sites, the definition of first and second being arbitrary. Cheers Thibaut ________________________________________ From: Yan Hou [yan.hou at nhm.uio.no] Sent: 13 January 2015 19:27 To: Jombart, Thibaut; adegenet-forum at lists.r-forge.r-project.org Subject: Re: [adegenet-forum] glPlot: which sample is used as the reference? Hi, Thanks a lot for your reply! I am sorry, but I might do not describe my question clearly. My question is: which sequence was chosen as the reference when using the glPlot? The plot implies the existence of a reference sequence (i.e. a missing site in relation to what? A SNP in relation to what?), right? Cheers, Yan On 13.01.2015 18:58, Jombart, Thibaut wrote: > > Hi there, > individuals are plotted according to their order in the genlight object > (individuals' indices are indicated on the y-axis. > Cheers > Thibaut > > ------------------------------------------------------------------------ > *From:* adegenet-forum-bounces at lists.r-forge.r-project.org > [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Yan > Hou [yan.hou at nhm.uio.no] > *Sent:* 12 January 2015 21:26 > *To:* adegenet-forum at lists.r-forge.r-project.org > *Cc:* Yan Hou > *Subject:* [adegenet-forum] glPlot: which sample is used as the reference? > > Hi, > I managed to use glPlot( SNPs,posi="topleft" ) to present the position > of SNPs in my concatenated and aligned RAD-seq data matrix. When looking > at the figure, I wonder which sample was used as the reference? The > first sample in the input file or the sample with most complete sequence > data? My first sample has a large number of missing data, so I wonder? > > Cheers, > > Yan From yan.hou at nhm.uio.no Tue Jan 13 20:27:43 2015 From: yan.hou at nhm.uio.no (Yan Hou) Date: Tue, 13 Jan 2015 20:27:43 +0100 Subject: [adegenet-forum] glPlot: which sample is used as the reference? In-Reply-To: <2CB2DA8E426F3541AB1907F98ABA6570ABEBD849@icexch-m1.ic.ac.uk> References: <54B43BEC.3020202@nhm.uio.no> <2CB2DA8E426F3541AB1907F98ABA6570ABEBD849@icexch-m1.ic.ac.uk> Message-ID: <54B571AF.5010300@nhm.uio.no> Hi, Thanks a lot for your reply! I am sorry, but I might do not describe my question clearly. My question is: which sequence was chosen as the reference when using the glPlot? The plot implies the existence of a reference sequence (i.e. a missing site in relation to what? A SNP in relation to what?), right? Cheers, Yan On 13.01.2015 18:58, Jombart, Thibaut wrote: > > Hi there, > individuals are plotted according to their order in the genlight object > (individuals' indices are indicated on the y-axis. > Cheers > Thibaut > > ------------------------------------------------------------------------ > *From:* adegenet-forum-bounces at lists.r-forge.r-project.org > [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Yan > Hou [yan.hou at nhm.uio.no] > *Sent:* 12 January 2015 21:26 > *To:* adegenet-forum at lists.r-forge.r-project.org > *Cc:* Yan Hou > *Subject:* [adegenet-forum] glPlot: which sample is used as the reference? > > Hi, > I managed to use glPlot( SNPs,posi="topleft" ) to present the position > of SNPs in my concatenated and aligned RAD-seq data matrix. When looking > at the figure, I wonder which sample was used as the reference? The > first sample in the input file or the sample with most complete sequence > data? My first sample has a large number of missing data, so I wonder? > > Cheers, > > Yan From yan.hou at nhm.uio.no Tue Jan 27 14:52:40 2015 From: yan.hou at nhm.uio.no (Yan Hou) Date: Tue, 27 Jan 2015 14:52:40 +0100 Subject: [adegenet-forum] glPlot: which sample is used as the reference? In-Reply-To: <2CB2DA8E426F3541AB1907F98ABA6570ABEBDC28@icexch-m1.ic.ac.uk> References: <54B43BEC.3020202@nhm.uio.no> <2CB2DA8E426F3541AB1907F98ABA6570ABEBD849@icexch-m1.ic.ac.uk>, <54B571AF.5010300@nhm.uio.no> <2CB2DA8E426F3541AB1907F98ABA6570ABEBDC28@icexch-m1.ic.ac.uk> Message-ID: <54C79828.4000509@nhm.uio.no> Hi, Thanks a lot for your explanation! So, the reference sequence was arbitrary, right? Cheers, Yan On 15.01.2015 16:42, Jombart, Thibaut wrote: > Hi there, > > I suspected this misunderstanding. genlight stores biallelic data are coded as binary, so the first allele is 0 and the second is 1 for all sites, the definition of first and second being arbitrary. > > Cheers > Thibaut > ________________________________________ > From: Yan Hou [yan.hou at nhm.uio.no] > Sent: 13 January 2015 19:27 > To: Jombart, Thibaut; adegenet-forum at lists.r-forge.r-project.org > Subject: Re: [adegenet-forum] glPlot: which sample is used as the reference? > > Hi, > Thanks a lot for your reply! I am sorry, but I might do not describe my > question clearly. > > My question is: which sequence was chosen as the reference when using > the glPlot? > > The plot implies the existence of a reference sequence (i.e. a missing > site in relation to what? A SNP in relation to what?), right? > > Cheers, > > Yan > > > > On 13.01.2015 18:58, Jombart, Thibaut wrote: >> >> Hi there, >> individuals are plotted according to their order in the genlight object >> (individuals' indices are indicated on the y-axis. >> Cheers >> Thibaut >> >> ------------------------------------------------------------------------ >> *From:* adegenet-forum-bounces at lists.r-forge.r-project.org >> [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Yan >> Hou [yan.hou at nhm.uio.no] >> *Sent:* 12 January 2015 21:26 >> *To:* adegenet-forum at lists.r-forge.r-project.org >> *Cc:* Yan Hou >> *Subject:* [adegenet-forum] glPlot: which sample is used as the reference? >> >> Hi, >> I managed to use glPlot( SNPs,posi="topleft" ) to present the position >> of SNPs in my concatenated and aligned RAD-seq data matrix. When looking >> at the figure, I wonder which sample was used as the reference? The >> first sample in the input file or the sample with most complete sequence >> data? My first sample has a large number of missing data, so I wonder? >> >> Cheers, >> >> Yan > From kwatt22 at uwo.ca Wed Jan 28 00:38:13 2015 From: kwatt22 at uwo.ca (Kaitlin Marie Watt) Date: Tue, 27 Jan 2015 18:38:13 -0500 Subject: [adegenet-forum] Different scatterplots each time (DAPC scatterplot) In-Reply-To: <72f0beb311f40.54c82103@uwo.ca> References: <73608ce514106.54c8208a@uwo.ca> <72d0936412206.54c820c6@uwo.ca> <72f0beb311f40.54c82103@uwo.ca> Message-ID: <7250e6c810055.54c7db15@uwo.ca> Hello, I?ve made a DAPC?scatterplot?using my microsatellite genotypes. However, when I run through the exact same code with the exact same parameters (No. clusters, No. of retained PCs, No. DFs), I get slightly different?scatterplots?each time (however, they are all similar in that none of them show much differentiation between clusters). Is this to be expected? And would someone please be able to explain (statistically) why I am getting slightly different results each time? Thank you in advance! Kaitlin -------------- next part -------------- An HTML attachment was scrubbed... URL: From t.jombart at imperial.ac.uk Wed Jan 28 12:40:52 2015 From: t.jombart at imperial.ac.uk (Jombart, Thibaut) Date: Wed, 28 Jan 2015 11:40:52 +0000 Subject: [adegenet-forum] Different scatterplots each time (DAPC scatterplot) In-Reply-To: <7250e6c810055.54c7db15@uwo.ca> References: <73608ce514106.54c8208a@uwo.ca> <72d0936412206.54c820c6@uwo.ca> <72f0beb311f40.54c82103@uwo.ca>,<7250e6c810055.54c7db15@uwo.ca> Message-ID: <2CB2DA8E426F3541AB1907F98ABA6570ABECBBD6@icexch-m1.ic.ac.uk> Hi Kaitlin, PCA and DAPC solution will not change except for the sign of the axes, which is arbitrary. Only the distances between the points (individuals) matter. The only possible stochastic thing here is if you use k-means clustering (find.clusters), which uses random starting states and therefore will not necessary give you the same results all the time (though qualitative changes are unlikely). Best Thibaut ________________________________ From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Kaitlin Marie Watt [kwatt22 at uwo.ca] Sent: 27 January 2015 23:38 To: adegenet-forum at lists.r-forge.r-project.org Subject: [adegenet-forum] Different scatterplots each time (DAPC scatterplot) Hello, I?ve made a DAPC scatterplot using my microsatellite genotypes. However, when I run through the exact same code with the exact same parameters (No. clusters, No. of retained PCs, No. DFs), I get slightly different scatterplots each time (however, they are all similar in that none of them show much differentiation between clusters). Is this to be expected? And would someone please be able to explain (statistically) why I am getting slightly different results each time? Thank you in advance! Kaitlin -------------- next part -------------- An HTML attachment was scrubbed... URL: From t.jombart at imperial.ac.uk Wed Jan 28 15:20:24 2015 From: t.jombart at imperial.ac.uk (Jombart, Thibaut) Date: Wed, 28 Jan 2015 14:20:24 +0000 Subject: [adegenet-forum] glPlot: which sample is used as the reference? In-Reply-To: <54C79828.4000509@nhm.uio.no> References: <54B43BEC.3020202@nhm.uio.no> <2CB2DA8E426F3541AB1907F98ABA6570ABEBD849@icexch-m1.ic.ac.uk>, <54B571AF.5010300@nhm.uio.no> <2CB2DA8E426F3541AB1907F98ABA6570ABEBDC28@icexch-m1.ic.ac.uk>, <54C79828.4000509@nhm.uio.no> Message-ID: <2CB2DA8E426F3541AB1907F98ABA6570ABECBCAF@icexch-m1.ic.ac.uk> I don't know how to rephrase my previous reply more explicitly. The choice of the 'reference' SNPs is arbitrary. There is no reference sequence used, but the one implied by the coding is arbitrary. Cheers Thibaut ________________________________________ From: Yan Hou [yan.hou at nhm.uio.no] Sent: 27 January 2015 13:52 To: Jombart, Thibaut; adegenet-forum at lists.r-forge.r-project.org Subject: Re: [adegenet-forum] glPlot: which sample is used as the reference? Hi, Thanks a lot for your explanation! So, the reference sequence was arbitrary, right? Cheers, Yan On 15.01.2015 16:42, Jombart, Thibaut wrote: > Hi there, > > I suspected this misunderstanding. genlight stores biallelic data are coded as binary, so the first allele is 0 and the second is 1 for all sites, the definition of first and second being arbitrary. > > Cheers > Thibaut > ________________________________________ > From: Yan Hou [yan.hou at nhm.uio.no] > Sent: 13 January 2015 19:27 > To: Jombart, Thibaut; adegenet-forum at lists.r-forge.r-project.org > Subject: Re: [adegenet-forum] glPlot: which sample is used as the reference? > > Hi, > Thanks a lot for your reply! I am sorry, but I might do not describe my > question clearly. > > My question is: which sequence was chosen as the reference when using > the glPlot? > > The plot implies the existence of a reference sequence (i.e. a missing > site in relation to what? A SNP in relation to what?), right? > > Cheers, > > Yan > > > > On 13.01.2015 18:58, Jombart, Thibaut wrote: >> >> Hi there, >> individuals are plotted according to their order in the genlight object >> (individuals' indices are indicated on the y-axis. >> Cheers >> Thibaut >> >> ------------------------------------------------------------------------ >> *From:* adegenet-forum-bounces at lists.r-forge.r-project.org >> [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Yan >> Hou [yan.hou at nhm.uio.no] >> *Sent:* 12 January 2015 21:26 >> *To:* adegenet-forum at lists.r-forge.r-project.org >> *Cc:* Yan Hou >> *Subject:* [adegenet-forum] glPlot: which sample is used as the reference? >> >> Hi, >> I managed to use glPlot( SNPs,posi="topleft" ) to present the position >> of SNPs in my concatenated and aligned RAD-seq data matrix. When looking >> at the figure, I wonder which sample was used as the reference? The >> first sample in the input file or the sample with most complete sequence >> data? My first sample has a large number of missing data, so I wonder? >> >> Cheers, >> >> Yan > From maria.guerrina at edu.unige.it Wed Jan 28 15:46:22 2015 From: maria.guerrina at edu.unige.it (Maria Guerrina) Date: Wed, 28 Jan 2015 15:46:22 +0100 Subject: [adegenet-forum] add pop info Message-ID: <90353040-59D7-41A9-8889-7FA27330F66A@edu.unige.it> Hi all! I have a vcf file with SNPs, but in this file there isn't the information about the populations. I converted the vcf format in a object of class "genind" using pegas package. I would like to know if it is possible to assign each individual to a population. Thank you! Best, Maria -- Maria Guerrina PhD Student Universit? di Genova DISTAV Corso Dogali 1M I - 16136 GENOVA (Italy) maria.guerrina at edu.unige.it -------------- next part -------------- An HTML attachment was scrubbed... URL: From t.jombart at imperial.ac.uk Wed Jan 28 16:18:34 2015 From: t.jombart at imperial.ac.uk (Jombart, Thibaut) Date: Wed, 28 Jan 2015 15:18:34 +0000 Subject: [adegenet-forum] add pop info In-Reply-To: <90353040-59D7-41A9-8889-7FA27330F66A@edu.unige.it> References: <90353040-59D7-41A9-8889-7FA27330F66A@edu.unige.it> Message-ID: <2CB2DA8E426F3541AB1907F98ABA6570ABECBD2C@icexch-m1.ic.ac.uk> Hello, please check the basics tutorial, especially section 3.3 on accessors. 'pop' is the one you want to use - example provided p13. Though it may seem dull, going through the basics tutorial will save you a lot of time if you use adegenet for data analysis. Cheers Thibaut ________________________________ From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Maria Guerrina [maria.guerrina at edu.unige.it] Sent: 28 January 2015 14:46 To: adegenet-forum at lists.r-forge.r-project.org Subject: [adegenet-forum] add pop info Hi all! I have a vcf file with SNPs, but in this file there isn't the information about the populations. I converted the vcf format in a object of class "genind" using pegas package. I would like to know if it is possible to assign each individual to a population. Thank you! Best, Maria -- Maria Guerrina PhD Student Universit? di Genova DISTAV Corso Dogali 1M I - 16136 GENOVA (Italy) maria.guerrina at edu.unige.it -------------- next part -------------- An HTML attachment was scrubbed... URL: From yan.hou at nhm.uio.no Wed Jan 28 15:27:30 2015 From: yan.hou at nhm.uio.no (Yan Hou) Date: Wed, 28 Jan 2015 15:27:30 +0100 Subject: [adegenet-forum] glPlot: which sample is used as the reference? In-Reply-To: <2CB2DA8E426F3541AB1907F98ABA6570ABECBCAF@icexch-m1.ic.ac.uk> References: <54B43BEC.3020202@nhm.uio.no> <2CB2DA8E426F3541AB1907F98ABA6570ABEBD849@icexch-m1.ic.ac.uk>, <54B571AF.5010300@nhm.uio.no> <2CB2DA8E426F3541AB1907F98ABA6570ABEBDC28@icexch-m1.ic.ac.uk>, <54C79828.4000509@nhm.uio.no> <2CB2DA8E426F3541AB1907F98ABA6570ABECBCAF@icexch-m1.ic.ac.uk> Message-ID: <54C8F1D2.2070402@nhm.uio.no> Thanks a lot! It is very clear now. Yan On 28.01.2015 15:20, Jombart, Thibaut wrote: > > I don't know how to rephrase my previous reply more explicitly. > > The choice of the 'reference' SNPs is arbitrary. There is no reference sequence used, but the one implied by the coding is arbitrary. > > Cheers > Thibaut > ________________________________________ > From: Yan Hou [yan.hou at nhm.uio.no] > Sent: 27 January 2015 13:52 > To: Jombart, Thibaut; adegenet-forum at lists.r-forge.r-project.org > Subject: Re: [adegenet-forum] glPlot: which sample is used as the reference? > > Hi, > Thanks a lot for your explanation! So, the reference sequence was > arbitrary, right? > > Cheers, > > Yan > > > On 15.01.2015 16:42, Jombart, Thibaut wrote: >> Hi there, >> >> I suspected this misunderstanding. genlight stores biallelic data are coded as binary, so the first allele is 0 and the second is 1 for all sites, the definition of first and second being arbitrary. >> >> Cheers >> Thibaut >> ________________________________________ >> From: Yan Hou [yan.hou at nhm.uio.no] >> Sent: 13 January 2015 19:27 >> To: Jombart, Thibaut; adegenet-forum at lists.r-forge.r-project.org >> Subject: Re: [adegenet-forum] glPlot: which sample is used as the reference? >> >> Hi, >> Thanks a lot for your reply! I am sorry, but I might do not describe my >> question clearly. >> >> My question is: which sequence was chosen as the reference when using >> the glPlot? >> >> The plot implies the existence of a reference sequence (i.e. a missing >> site in relation to what? A SNP in relation to what?), right? >> >> Cheers, >> >> Yan >> >> >> >> On 13.01.2015 18:58, Jombart, Thibaut wrote: >>> >>> Hi there, >>> individuals are plotted according to their order in the genlight object >>> (individuals' indices are indicated on the y-axis. >>> Cheers >>> Thibaut >>> >>> ------------------------------------------------------------------------ >>> *From:* adegenet-forum-bounces at lists.r-forge.r-project.org >>> [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Yan >>> Hou [yan.hou at nhm.uio.no] >>> *Sent:* 12 January 2015 21:26 >>> *To:* adegenet-forum at lists.r-forge.r-project.org >>> *Cc:* Yan Hou >>> *Subject:* [adegenet-forum] glPlot: which sample is used as the reference? >>> >>> Hi, >>> I managed to use glPlot( SNPs,posi="topleft" ) to present the position >>> of SNPs in my concatenated and aligned RAD-seq data matrix. When looking >>> at the figure, I wonder which sample was used as the reference? The >>> first sample in the input file or the sample with most complete sequence >>> data? My first sample has a large number of missing data, so I wonder? >>> >>> Cheers, >>> >>> Yan >> >