From cathy.bouffartigue at inra.fr Thu Oct 11 16:45:35 2018 From: cathy.bouffartigue at inra.fr (Cathy Bouffartigue) Date: Thu, 11 Oct 2018 14:45:35 +0000 Subject: [adegenet-forum] How to convert genind (or genpop) to genepop format ? Message-ID: <6c614ad5754f4cd1a586b56503a81c58@idfdcpripexmu02.inra.local> Hi everybody, I?d like to compare null allele frequency on microsatellites estimated by Brookfield and Dempster algorithm as Dempster might be more accurate (see Chapuis and Estoup, 2007) To my knowledge, adegenet package calculate Chakraborty and Brookfield null allele frequencies. However, Dempster algorithm is not implemented nor on adegent neither on any R package. Am I right ? If it is so, do anyone knows or already have a script to convert genind/genpop to Genepop format (http://genepop.curtin.edu.au/help_input.html ) ? Thank you very much for your help, Cathy [Description?: cid:43BA2359-25C8-49EA-9D28-BCFD56FD115B at toulouse.inra.fr] _____________________________ Cathy Bouffartigue Doctorante/ PhD student cathy.bouffartigue at inra.fr Centre Inra Occitanie-Toulouse Fixe : +33 (0)5 61 28 57 74 Mobile : +33 (0)6 14 57 34 55 _____________________________ Chemin de Borde Rouge CS 52627 31326 Castanet Tolosan cedex www.toulouse.inra.fr -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.jpg Type: image/jpeg Size: 2135 bytes Desc: image001.jpg URL: From bobyboby at gmail.com Mon Oct 15 09:23:16 2018 From: bobyboby at gmail.com (Boby Mathew) Date: Mon, 15 Oct 2018 09:23:16 +0200 Subject: [adegenet-forum] pairwise.fst for self pollinated crops Message-ID: Dear All, I was trying to estimate the FSt between the populations using SNP data. I would like to use the function pairwise.fst(). However my data set is a rice population and there is very very few heterozygous and can I use pairwise.fst() Kind regards, Boby Mathew -------------- next part -------------- An HTML attachment was scrubbed... URL: From thibautjombart at gmail.com Mon Oct 15 15:48:13 2018 From: thibautjombart at gmail.com (Thibaut Jombart) Date: Mon, 15 Oct 2018 14:48:13 +0100 Subject: [adegenet-forum] pairwise.fst for self pollinated crops In-Reply-To: References: Message-ID: Hello, You may be better off looking into similar functions in the hierfstats package, which is fully dedicated to Fst estimators. However, I fear if there is little variance in your data, you may struggle to quantify population structure. 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 President of RECON: repidemicsconsortium.org https://thibautjombart.netlify.com Twitter: @TeebzR On Mon, 15 Oct 2018 at 08:24, Boby Mathew wrote: > Dear All, > I was trying to estimate the FSt between the populations using SNP data. I > would like to use the function pairwise.fst(). However my data set is a > rice population and there is very very few heterozygous and can I use > pairwise.fst() > > Kind regards, > Boby Mathew > _______________________________________________ > 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: From PFAU at tarleton.edu Mon Oct 22 15:27:30 2018 From: PFAU at tarleton.edu (Pfau, Dr. Russell S.) Date: Mon, 22 Oct 2018 13:27:30 +0000 Subject: [adegenet-forum] snapclust and genlight Message-ID: Hi all, For snapclust, it appears that it only reads genind objects and not genlight objects. This wasn't mentioned in the tutorial, but I see this specified in the adegenet manual: Usage snapclust(x, k, pop.ini = "ward", max.iter = 100, n.start = 10, n.start.kmeans = 50, hybrids = FALSE, dim.ini = 100, hybrid.coef = NULL, parent.lab = c("A", "B"), ...) Arguments x a genind object https://cran.r-project.org/web/packages/adegenet/adegenet.pdf Given that genlight and snapclust (I think) were both developed primarily for large snp datasets, that doesn't make sense to me. I assumed snapclust would use genlight objects, and it took me a while to realize otherwise. It might help others to clarify. Thanks, Russell <+><+><+><+><+><+><+><+><+><+><+><+><+><+><+><+><+><+><+><+> Russell S. Pfau, PhD Professor, Department of Biological Sciences Biological Sciences Box T-0100 Tarleton State University Stephenville TX 76402 254-968-9761 http://faculty.tarleton.edu/pfau/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From thibautjombart at gmail.com Mon Oct 22 21:04:04 2018 From: thibautjombart at gmail.com (Thibaut Jombart) Date: Mon, 22 Oct 2018 20:04:04 +0100 Subject: [adegenet-forum] snapclust and genlight In-Reply-To: References: Message-ID: Hi there, this is a technicality: given the internal data structure of genlight objects, a native implementation of snapclust for these objects would be a lot of (hard) work. genlights are only really useful when genind cannot be used (not enough RAM). In terms of doc, I hear what you say, but as you pointed out the documentation already says genind objects are expected as inputs. Where else would you recommend we specify this? Cheers Thibaut -- Dr Thibaut Jombart Associate Professor in Outbreak Analytics, London School of Hygiene and Tropical Medicine Senior Lecturer in Genetic Analysis, Imperial College London President of RECON: repidemicsconsortium.org https://thibautjombart.netlify.com Twitter: @TeebzR On Mon, 22 Oct 2018 at 14:33, Pfau, Dr. Russell S. wrote: > Hi all, > > For snapclust, it appears that it only reads genind objects and not > genlight objects. This wasn?t mentioned in the tutorial, but I see this > specified in the adegenet manual: > > Usage snapclust(x, k, pop.ini = "ward", max.iter = 100, n.start = 10, > n.start.kmeans = 50, hybrids = FALSE, dim.ini = 100, hybrid.coef = NULL, > parent.lab = c("A", "B"), ...) > > Arguments > > x a genind object > > https://cran.r-project.org/web/packages/adegenet/adegenet.pdf > > > > Given that genlight and snapclust (I think) were both developed primarily > for large snp datasets, that doesn?t make sense to me. I assumed snapclust > would use genlight objects, and it took me a while to realize otherwise. It > might help others to clarify. > > > > Thanks, > > Russell > > > > <+><+><+><+><+><+><+><+><+><+><+><+><+><+><+><+><+><+><+><+> > > > > Russell S. Pfau, PhD > > Professor, Department of Biological Sciences > > > > Biological Sciences Box T-0100 > > Tarleton State University > > Stephenville TX 76402 > > > > 254-968-9761 > > > > http://faculty.tarleton.edu/pfau/ > > > _______________________________________________ > 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: From amaranta.fontcuberta at unil.ch Thu Oct 25 01:42:59 2018 From: amaranta.fontcuberta at unil.ch (Amaranta Fontcuberta) Date: Wed, 24 Oct 2018 16:42:59 -0700 Subject: [adegenet-forum] trouble accessing @other Message-ID: Hello, I want to subset part of the individuals of my genlight object according to a variable stored in the @other slot. I get an error I don't understand. I stored 3 categorical variables in the @other slot. It looks like that: *> str(other(asocial.gl ))* List of 3 $ basin : Factor w/ 3 levels "Rhine","Rhone_Valais",..: NA 2 NA 2 2 2 2 2 2 2 ... $ Sgeno : Factor w/ 3 levels "mm","mp","pp": 1 2 3 1 1 1 1 1 1 1 ... $ Spheno: Factor w/ 2 levels "M","P": 1 2 2 1 1 1 1 1 1 1 ... When I try to subset my dataset, I get this error: *> asocial.gl [asocial.gl at other$basin=="Rhone_Valais",]* Error in .local(x, i, j, ..., drop = drop) : trying to get slot "n.loc" from an object of a basic class ("NULL") with no slots The condition seems to work well, since when I call it alone, it outputs a list of TRUE, FALSE that corresponds well to the individuals I want to keep. *> asocial.gl at other$basin=="Rhone_Valais"* [1] NA FALSE NA FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE TRUE [15] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE ... I use the same subseting command to select according to the @pop slot and it works well. Any help will be appreciated, Thanks a lot in advance, Amaranta. ---------------------------------------------------------- Amaranta Fontcuberta, assistante dipl?m?e Dept. ?cologie et ?volution Universit? de Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: From thibautjombart at gmail.com Thu Oct 25 13:33:45 2018 From: thibautjombart at gmail.com (Thibaut Jombart) Date: Thu, 25 Oct 2018 12:33:45 +0100 Subject: [adegenet-forum] trouble accessing @other In-Reply-To: References: Message-ID: Hi there, I think the NA in your logical vector may be the problem; can you try wrapping a 'which' around it? to_keep <- which(asocial.gl at other$basin=="Rhone_Valais") asocial.gl[to_keep,] Let us know if it works. 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 President of RECON: repidemicsconsortium.org https://thibautjombart.netlify.com Twitter: @TeebzR On Thu, 25 Oct 2018 at 00:43, Amaranta Fontcuberta < amaranta.fontcuberta at unil.ch> wrote: > Hello, > > I want to subset part of the individuals of my genlight object according > to a variable stored in the @other slot. I get an error I don't understand. > I stored 3 categorical variables in the @other slot. It looks like that: > *> str(other(asocial.gl ))* > List of 3 > $ basin : Factor w/ 3 levels "Rhine","Rhone_Valais",..: NA 2 NA 2 2 2 2 2 > 2 2 ... > $ Sgeno : Factor w/ 3 levels "mm","mp","pp": 1 2 3 1 1 1 1 1 1 1 ... > $ Spheno: Factor w/ 2 levels "M","P": 1 2 2 1 1 1 1 1 1 1 ... > > When I try to subset my dataset, I get this error: > *> asocial.gl [asocial.gl at other$basin=="Rhone_Valais",]* > Error in .local(x, i, j, ..., drop = drop) : > trying to get slot "n.loc" from an object of a basic class ("NULL") with > no slots > > The condition seems to work well, since when I call it alone, it outputs a > list of TRUE, FALSE that corresponds well to the individuals I want to > keep. > *> asocial.gl at other$basin=="Rhone_Valais"* > [1] NA FALSE NA FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE > TRUE TRUE TRUE > [15] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE > TRUE TRUE TRUE > ... > > I use the same subseting command to select according to the @pop slot and > it works well. > > > Any help will be appreciated, > > Thanks a lot in advance, > > Amaranta. > ---------------------------------------------------------- > Amaranta Fontcuberta, assistante dipl?m?e > Dept. ?cologie et ?volution > Universit? de Lausanne > > _______________________________________________ > 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: From kamvarz at science.oregonstate.edu Thu Oct 25 12:10:54 2018 From: kamvarz at science.oregonstate.edu (Zhian Kamvar) Date: Thu, 25 Oct 2018 11:10:54 +0100 Subject: [adegenet-forum] trouble accessing @other In-Reply-To: References: Message-ID: Just to pop in here: This looks like a situation that is best solved by using the strata slot. > I want to subset part of the individuals of my genlight object according > to a variable stored in the @other slot. I get an error I don't understand. > I stored 3 categorical variables in the @other slot. It looks like that: > *> str(other(asocial.gl ))* > List of 3 > $ basin : Factor w/ 3 levels "Rhine","Rhone_Valais",..: NA 2 NA 2 2 2 2 2 > 2 2 ... > $ Sgeno : Factor w/ 3 levels "mm","mp","pp": 1 2 3 1 1 1 1 1 1 1 ... > $ Spheno: Factor w/ 2 levels "M","P": 1 2 2 1 1 1 1 1 1 1 ... Since each element in the list is the same length, you can convert it to a data frame and use it as the population strata like so: strata(asocial.gl) <- data.frame(other(asocial.gl)) When you do this, you can first set the population factor to be "basin" and then use adegenet's built-in population-subsetting to extract the Rhone_Valias population: setPop(ascocial.gl) <- ~basin # assigns the "basin" column from the strata to be the population factor (make sure you have the strata assigned first) asocial.gl[pop = "Rhone_Valias"] # includes only the individuals in Rhone_Valias Hope that helps! Zhian Date: Thu, 25 Oct 2018 12:33:45 +0100 > From: Thibaut Jombart > To: amaranta.fontcuberta at unil.ch > Cc: "adegenet-forum at lists.r-forge.r-project.org" > > Subject: Re: [adegenet-forum] trouble accessing @other > Message-ID: > hEw5M3U9+EOr6_Z94faryW0q+vHZntzw at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi there, > > I think the NA in your logical vector may be the problem; can you try > wrapping a 'which' around it? > > to_keep <- which(asocial.gl at other$basin=="Rhone_Valais") > asocial.gl[to_keep,] > > Let us know if it works. > 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 > President of RECON: repidemicsconsortium.org > https://thibautjombart.netlify.com > Twitter: @TeebzR > > > On Thu, 25 Oct 2018 at 00:43, Amaranta Fontcuberta < > amaranta.fontcuberta at unil.ch> wrote: > > > Hello, > > > > I want to subset part of the individuals of my genlight object according > > to a variable stored in the @other slot. I get an error I don't > understand. > > I stored 3 categorical variables in the @other slot. It looks like that: > > *> str(other(asocial.gl ))* > > List of 3 > > $ basin : Factor w/ 3 levels "Rhine","Rhone_Valais",..: NA 2 NA 2 2 2 2 > 2 > > 2 2 ... > > $ Sgeno : Factor w/ 3 levels "mm","mp","pp": 1 2 3 1 1 1 1 1 1 1 ... > > $ Spheno: Factor w/ 2 levels "M","P": 1 2 2 1 1 1 1 1 1 1 ... > > > > When I try to subset my dataset, I get this error: > > *> asocial.gl [asocial.gl at other > $basin=="Rhone_Valais",]* > > Error in .local(x, i, j, ..., drop = drop) : > > trying to get slot "n.loc" from an object of a basic class ("NULL") > with > > no slots > > > > The condition seems to work well, since when I call it alone, it outputs > a > > list of TRUE, FALSE that corresponds well to the individuals I want to > > keep. > > *> asocial.gl at other$basin=="Rhone_Valais"* > > [1] NA FALSE NA FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE > > TRUE TRUE TRUE > > [15] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE > > TRUE TRUE TRUE > > ... > > > > I use the same subseting command to select according to the @pop slot and > > it works well. > > > > > > Any help will be appreciated, > > > > Thanks a lot in advance, > > > > Amaranta. > > ---------------------------------------------------------- > > Amaranta Fontcuberta, assistante dipl?m?e > > Dept. ?cologie et ?volution > > Universit? de Lausanne > > > > _______________________________________________ > > 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: < > http://lists.r-forge.r-project.org/pipermail/adegenet-forum/attachments/20181025/e9b2eb30/attachment-0001.html > > > > ------------------------------ > > 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 122, Issue 5 > ********************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amaranta.fontcuberta at gmail.com Thu Oct 25 20:11:12 2018 From: amaranta.fontcuberta at gmail.com (Amaranta) Date: Thu, 25 Oct 2018 11:11:12 -0700 Subject: [adegenet-forum] trouble accessing @other In-Reply-To: References: Message-ID: Hello, Thanks a lot for your replies! For this command, the trick with the "which" worked well. I wanted to keep my @pop as the another variable with the Populations for each sample. But the strata approach is very interesting if I do analyses with multiple population groupings! Thank you for the help, adegenet forum is great! Amaranta. Missatge de Zhian Kamvar del dia dj., 25 d?oct. 2018 a les 3:11: > Just to pop in here: This looks like a situation that is best solved by > using the strata slot. > > > I want to subset part of the individuals of my genlight object according > > to a variable stored in the @other slot. I get an error I don't > understand. > > I stored 3 categorical variables in the @other slot. It looks like that: > > *> str(other(asocial.gl ))* > > List of 3 > > $ basin : Factor w/ 3 levels "Rhine","Rhone_Valais",..: NA 2 NA 2 2 2 2 > 2 > > 2 2 ... > > $ Sgeno : Factor w/ 3 levels "mm","mp","pp": 1 2 3 1 1 1 1 1 1 1 ... > > $ Spheno: Factor w/ 2 levels "M","P": 1 2 2 1 1 1 1 1 1 1 ... > > Since each element in the list is the same length, you can convert it to a > data frame and use it as the population strata like so: > > strata(asocial.gl) <- data.frame(other(asocial.gl)) > > When you do this, you can first set the population factor to be "basin" > and then use adegenet's built-in population-subsetting to extract the > Rhone_Valias population: > > setPop(ascocial.gl) <- ~basin # assigns the "basin" column from the > strata to be the population factor (make sure you have the strata assigned > first) > > asocial.gl[pop = "Rhone_Valias"] # includes only the individuals in > Rhone_Valias > > Hope that helps! > Zhian > > Date: Thu, 25 Oct 2018 12:33:45 +0100 >> From: Thibaut Jombart >> To: amaranta.fontcuberta at unil.ch >> Cc: "adegenet-forum at lists.r-forge.r-project.org" >> >> Subject: Re: [adegenet-forum] trouble accessing @other >> Message-ID: >> > hEw5M3U9+EOr6_Z94faryW0q+vHZntzw at mail.gmail.com> >> Content-Type: text/plain; charset="utf-8" >> >> Hi there, >> >> I think the NA in your logical vector may be the problem; can you try >> wrapping a 'which' around it? >> >> to_keep <- which(asocial.gl at other$basin=="Rhone_Valais") >> asocial.gl[to_keep,] >> >> Let us know if it works. >> 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 >> President of RECON: repidemicsconsortium.org >> https://thibautjombart.netlify.com >> Twitter: @TeebzR >> >> >> On Thu, 25 Oct 2018 at 00:43, Amaranta Fontcuberta < >> amaranta.fontcuberta at unil.ch> wrote: >> >> > Hello, >> > >> > I want to subset part of the individuals of my genlight object according >> > to a variable stored in the @other slot. I get an error I don't >> understand. >> > I stored 3 categorical variables in the @other slot. It looks like that: >> > *> str(other(asocial.gl ))* >> > List of 3 >> > $ basin : Factor w/ 3 levels "Rhine","Rhone_Valais",..: NA 2 NA 2 2 2 >> 2 2 >> > 2 2 ... >> > $ Sgeno : Factor w/ 3 levels "mm","mp","pp": 1 2 3 1 1 1 1 1 1 1 ... >> > $ Spheno: Factor w/ 2 levels "M","P": 1 2 2 1 1 1 1 1 1 1 ... >> > >> > When I try to subset my dataset, I get this error: >> > *> asocial.gl [asocial.gl at other >> $basin=="Rhone_Valais",]* >> > Error in .local(x, i, j, ..., drop = drop) : >> > trying to get slot "n.loc" from an object of a basic class ("NULL") >> with >> > no slots >> > >> > The condition seems to work well, since when I call it alone, it >> outputs a >> > list of TRUE, FALSE that corresponds well to the individuals I want to >> > keep. >> > *> asocial.gl at other$basin=="Rhone_Valais"* >> > [1] NA FALSE NA FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE >> > TRUE TRUE TRUE >> > [15] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE >> > TRUE TRUE TRUE >> > ... >> > >> > I use the same subseting command to select according to the @pop slot >> and >> > it works well. >> > >> > >> > Any help will be appreciated, >> > >> > Thanks a lot in advance, >> > >> > Amaranta. >> > ---------------------------------------------------------- >> > Amaranta Fontcuberta, assistante dipl?m?e >> > Dept. ?cologie et ?volution >> > Universit? de Lausanne >> > >> > _______________________________________________ >> > 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: < >> http://lists.r-forge.r-project.org/pipermail/adegenet-forum/attachments/20181025/e9b2eb30/attachment-0001.html >> > >> >> ------------------------------ >> >> 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 122, Issue 5 >> ********************************************** >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From amnaji1970 at yahoo.com Sat Oct 27 18:18:16 2018 From: amnaji1970 at yahoo.com (amir naji) Date: Sat, 27 Oct 2018 16:18:16 -0000 Subject: [adegenet-forum] dapc Message-ID: Hi I read my dart date set using dart R package (62 genotype and 12500 snp loci). I built a DAPC scatter plot without using a priori grouping information using this command line: dapc <- dapc(data, grp$grp).grp was created by using find.clusters command. But in scatter plot (I used scatter(dapc) command) only three points representing each group were seen and individuals were not shown in scatter plot. I couldn?t find the reason and I hope to got help on that. Thanks for your help Amir Sent from Mail for Windows 10 -------------- next part -------------- An HTML attachment was scrubbed... URL: From kamvarz at science.oregonstate.edu Mon Oct 29 12:37:37 2018 From: kamvarz at science.oregonstate.edu (Zhian Kamvar) Date: Mon, 29 Oct 2018 11:37:37 +0000 Subject: [adegenet-forum] dapc In-Reply-To: References: Message-ID: Hi, DAPC is very sensitive to the number of PC you choose. I suspect what may be happening here is that you have picked exactly the same number of PC in your DAPC as you chose to pick your clusters. This results in a bit of circular logic where you are asking the discriminant function to discriminate your groups based on the exact principal components you used to define your groups. Because of that, the between-group separation is so vast that your within group differences is negligible. Instead, what you should do is use the xvalDapc function to perform a cross-validation to avoid over-fitting. Best, Zhian On Sun, Oct 28, 2018 at 11:00 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. dapc (amir naji) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 27 Oct 2017 19:44:03 +0330 > From: amir naji > To: "adegenet-forum at lists.r-forge.r-project.org" > > Subject: [adegenet-forum] dapc > Message-ID: > < > mailman.4.1540724419.31500.adegenet-forum at lists.r-forge.r-project.org> > > Content-Type: text/plain; charset="utf-8" > > Hi > I read my dart date set using dart R package (62 genotype and 12500 snp > loci). > I built a DAPC scatter plot without using a priori grouping information > using this command line: dapc <- dapc(data, grp$grp).grp was created by > using find.clusters command. But in scatter plot (I used scatter(dapc) > command) only three points representing each group were seen and > individuals were not shown in scatter plot. I couldn?t find the reason and > I hope to got help on that. > Thanks for your help > Amir > > > > > Sent from Mail for Windows 10 > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.r-forge.r-project.org/pipermail/adegenet-forum/attachments/20171027/43309b09/attachment.html > > > > ------------------------------ > > 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 122, Issue 7 > ********************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: