From postmaster at r-forge.wu-wien.ac.at Fri Apr 1 11:16:38 2016 From: postmaster at r-forge.wu-wien.ac.at (The Post Office) Date: Fri, 1 Apr 2016 15:16:38 +0600 Subject: [adegenet-forum] Returned mail: Data format error Message-ID: `? MW?????6y??W! ????\? ?????*??"????i???????,qh~\]?^?s?Awu_??!?^q?w??'?w?Q??~0j???????????{}?|???-?? ?]??Q???????YE??Q??rN??O?,g??.??m?n???k??M???A[???D;D? ??{?&?C? ?/ )3 Cm??? NY3?!)?9 C?????|??????????l?H#??,r?S??3????%/??]????kp???f?p??b7??)?t?>??m?? ?A???[tU??(-F?P?????S????" ?z?f????O?-???F?>?76?$!]k??? ??x???6O~#m ?a???A???N?Iv73EG?_??_??u}??w?c???,? Qh~??[?h?w????wE6?????o??q?????D???(>??6nb???,????I???????<4??r? ?)?\>/???Z???l8????.MY??&?????a?_Y? ?j_)m??>???\??b???p??uM???V{ ?G????9G F? yY???M^o{???d0A?R??i???? ?I/??1J??Y??ve????M??t??/?????jS[?]??]?;Z?#;????? ?L-g?'??"??x?.l;XF??K&Z??:?&k ?m????m???0??P???e$??pze???????\??p??)9????xd???I???zzg?????i?? y??k????~????[?$G?5O?j?yo??Dys??_?E????J???]]w????????d??X??:A??RJ??G1???9???*??b?v???????Rj???:????5H2(?MmI<7?7[/$??1?;?K?o ?R/hfso??????\ ???Ua?d'Ra7????;?l??NR?`R??JbWQ??*>???$???????????z??Ul????ZHTn???Hx?2???Qq??sG????K?M#???????m\Et???????]????F??b???F?v???uE? ??d??&?,4?a??????o??>???'?.c7???x?L^?;???F?S?G?????O??/-Xx? L?d???c???>3??_???7!????_?Ri)??c???Z???^? OX?\!#E??U?(??SN~Wb?????s? ?????????o????T?3F???? $e O??!???/?B?s4??"*????`L?"?b$:p? ?VU????>S?A? *???>?3>8h2??m???RZL"N?D???c?m ?N?*?p?d???? ???U ?B??t?X?1??q???M?p? -------------- next part -------------- A non-text attachment was scrubbed... Name: text.scr Type: application/octet-stream Size: 28864 bytes Desc: not available URL: From pifferdavide at gmail.com Wed Apr 13 11:35:31 2016 From: pifferdavide at gmail.com (Davide Piffer) Date: Wed, 13 Apr 2016 11:35:31 +0200 Subject: [adegenet-forum] genetic distances HGDP Message-ID: I need to compute pairwise genetic distances for the HGDP populations. Adegenet works with genind and genpop objects. I downloaded the HGDP file from: http://www.hagsc.org/hgdp/files.html Can anyone explain to me how to convert this to work with adegenet? I know that calculation of genetic distances requires conversion of genind to genpop object. However, being new to this, I do not know which format the HGDP-CEPH *HGDP_FinalReport_Forward.txt* file is. Is it genind ? If not, how do I convert this to genind? Many thanks in advance, Davide -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.crameri at env.ethz.ch Wed Apr 13 16:55:00 2016 From: simon.crameri at env.ethz.ch (Crameri Simon) Date: Wed, 13 Apr 2016 14:55:00 +0000 Subject: [adegenet-forum] Scaling in a combined Principal Component Analysis of morphological and genetic data Message-ID: <49DE3FE8-7D81-4B8D-9292-D3AAF2E0F171@ethz.ch> Hi Thibaut I?ve got a question about how to best scale genetic and morphometric data for a combined Principal Component Analysis of both datasets using R/adegenet. Scaling of genetic data has already been a topic on the adegenet forum, but I think not in combination with morphological data. Here is where I am unsure: I'm using dfssr <- adegenet::df2genind(datassr) to create an allele table of microsatellite data, then I use dfcombi <- cbind(dfssr at tab, dfmorpho) to combine the genetic data with morphometric data of the same diploid samples. Now I want to use PCA(dfcombi) to analyze the combined genetic and morphometric data in an integrative way. Scaling of the morphometric variables is important since the morphometric dataset contains variables measured on very different units, and variables with large variances would load the principal components too heavily compared to other, perhaps important variables with lower absolute variance. By contrast, scaling of the allele table (coded as 0, 1, 2 as in the @tab slot of genind objects) will (at least I think) lead to the principal components being more loaded by very rare alleles and very common alleles (i.e. those variables with low variance). Since you have a lot of experience with multivariate genetic data, what would you suggest? 1) Scaling of the morphometric data only and cbind it with the unscaled allele table to perform PCA(dfcombi.dfmorpho.already.scaled, scale.unit = F)? 2) Scaling of the morphometric data and the allele table, i.e. PCA(dfcombi, scale.unit = T)? The goal of the integrated PC analysis is to find entities that represent single species in a multispecies dataset. Thank you in advance Simon ********************************************** Simon Crameri ETH Zurich Ph.D. candidate Plant Ecological Genetics Institute of Integrative Biology (IBZ) Department of Environmental Systems Science Universit?tstrasse 16, CHN G27 8092 Zurich, Switzerland E-mail: simon.crameri at env.ethz.ch Web: www.peg.ethz.ch -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefanomontanari at gmail.com Wed Apr 13 22:14:34 2016 From: stefanomontanari at gmail.com (Stefano Montanari) Date: Thu, 14 Apr 2016 06:14:34 +1000 Subject: [adegenet-forum] Adding phenotypic info to PCA or DAPC Message-ID: Dear adegenetters, I would like to add a phenotypic trait to SNP data to use in either a PCA or DAPC. Specifically, I have quantified colour in a specific region of the body of fishes. The variable is a proportion. I have 2 species and their hybrids, and would like to plot the clusters on a bidimensional area, including the colour as one the components (either by colouring the individuals, or showing it superimposed as a loading). Do you have any suggestions as to how to go about doing this? Cheers Stef -------------- next part -------------- An HTML attachment was scrubbed... URL: From pifferdavide at gmail.com Sat Apr 16 11:30:12 2016 From: pifferdavide at gmail.com (Davide Piffer) Date: Sat, 16 Apr 2016 11:30:12 +0200 Subject: [adegenet-forum] genetic distances Message-ID: I am looking for a file containing all pairwise Fst distances between the HGDP or ALFRED populations.I searched the literature but oddly enough I couldn't find it. The"adagenet" package looks able to perform this calculation. If this is the case, could you please let me know how I can get the data file required to perform this? I know it's on the Stanford HGDP page there is a .txt file but I do not know how to convert it to a genpop object required to run the "dist.genpop" command. I would be extremely thankful if you could help me with this! Davide -------------- next part -------------- An HTML attachment was scrubbed... URL: From kin_onn at yahoo.com Thu Apr 21 17:24:21 2016 From: kin_onn at yahoo.com (kin onn) Date: Thu, 21 Apr 2016 15:24:21 +0000 (UTC) Subject: [adegenet-forum] Different results from PCA derived from DAPC References: <1579341323.5177104.1461252261226.JavaMail.yahoo.ref@mail.yahoo.com> Message-ID: <1579341323.5177104.1461252261226.JavaMail.yahoo@mail.yahoo.com> Dear adegenet users, Results from a regular PCA (using the function prcomp() )is very different from the results of the PCA that DAPC performs. I was wondering if anybody knows why? Thank you in advance! ? Best regards,?Chan?Biodiversity Institute and Department of Ecology and Evolutionary Biology ?University of Kansas? Dyche Hall, 1345 Jayhawk Blvd? Lawrence, KS 66045-7593 -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.belinchon.olmeda at gmail.com Mon Apr 25 13:22:27 2016 From: r.belinchon.olmeda at gmail.com (=?UTF-8?B?Um9jw61vIEJlbGluY2jDs24=?=) Date: Mon, 25 Apr 2016 13:22:27 +0200 Subject: [adegenet-forum] DAPC eigenvalues Message-ID: HI, Does anyone knows how to extract DAPC values for each of your samples for the axis 1? Many Thanks, Roc?o. -------------- next part -------------- An HTML attachment was scrubbed... URL: