http://blog.gmane.org/gmane.comp.lang.r.genetics hourly 1 1901-01-01T00:00+00:00 http://gmane.org/img/gmane-25t.png http://gmane.org http://permalink.gmane.org/gmane.comp.lang.r.genetics/37 <pre>Dear All, a new version of MultiPhen (0.3) is available on CRAN, and will be available to a mirror near you soon. *Please upgrade* because this release is a bug fix release. A new version, with improvements in the output and more useful error messages is basically ready, but I will wait to release it until next week to add other possible improvements. For all asking for the related paper, Paul should be ready with the final draft 'soon'. Cheers Federico -- Federico C. F. Calboli Neuroepidemiology and Ageing Research Imperial College, St. Mary's Campus Norfolk Place, London W2 1PG Tel +44 (0)20 75941602 Fax +44 (0)20 75943193 f.calboli [.a.t] imperial.ac.uk f.calboli [.a.t] gmail.com </pre> Federico Calboli 2012-02-29T14:52:49 http://permalink.gmane.org/gmane.comp.lang.r.genetics/36 <pre>Dear List members, I have a question regarding the DAPC scatter. I have 8 sampled populations (from 8 geographic locations), and the DAPC analysis (as well as Structure), found 6 clusters. Now, these clusters are not separate geographically, which means that each sampled location has a proportion of each cluster. I wanted to see this on a scatter, to see how different clusters were, hence I plotted the $ind.coord (I used points()), and simply coloured the points by clustering this time (as per DAPC analysis) and not by geographic location. I was expecting to get same-colour points clustered close together (whereas in the first DAPC, where colours were based on geog location, they were all overlapping). Instead, colours remained all overlapping. I do not understand how this explains the existence of 6 clusters, if they're not there on the graph. Maybe my assumption that re-colouring the points by cluster (and not location) would present distinct groups was wrong? I hope what I say makes sense... I should say that I re-analysed from the start the same dataset too, this time grouping individuals by cluster assignment and not by geographical location, and I do get nicely separated clusters on the scatter. I thought this was wrong in principle though, as I was basing it on a new analysis. Cheers Ilaria </pre> Ilaria Coscia 2012-01-11T15:50:53 http://permalink.gmane.org/gmane.comp.lang.r.genetics/35 <pre>Hello, yes, genetics is still on CRAN but deprecated. Its functionalities are still available. There are quite a few options to do a HWE test: - (genetics): HWE.chisq, HWE.test, HWE.exact - (adegenet, wrapper for genetics): HWE.test.genind - (ape): hw.test ... Judging from the check results for genetics: http://cran.r-project.org/web/checks/check_results_genetics.html it seems likely that the package will remain on CRAN for a while, unless the maintainers decide otherwise. Cheers Thibaut ________________________________________ From: Federico Calboli [f.calboli-AQ/gCgVxFfnQzY9nttDBhA&lt; at &gt;public.gmane.org] Sent: 18 November 2011 12:30 To: Jombart, Thibaut Cc: r-sig-genetics-0bNBQ1PAWB4BXFe83j6qeQ&lt; at &gt;public.gmane.org Subject: Re: [R-sig-genetics] package mvtnorm is obsolete On 18 Nov 2011, at 12:22, Jombart, Thibaut wrote: genetics is still on CRAN btw Neither have the function genotype() and the corollary function as.genotype(), which are quite useful caculating HWE using other packages -- see hwe.hardy() in package gap. bw F -- Federico C. F. Calboli Neuroepidemiology and Ageing Research Imperial College, St. Mary's Campus Norfolk Place, London W2 1PG Tel +44 (0)20 75941602 Fax +44 (0)20 75943193 f.calboli [.a.t] imperial.ac.uk f.calboli [.a.t] gmail.com </pre> Jombart, Thibaut 2011-11-18T12:41:38 http://permalink.gmane.org/gmane.comp.lang.r.genetics/34 <pre> genetics is still on CRAN btw Neither have the function genotype() and the corollary function as.genotype(), which are quite useful caculating HWE using other packages -- see hwe.hardy() in package gap. bw F -- Federico C. F. Calboli Neuroepidemiology and Ageing Research Imperial College, St. Mary's Campus Norfolk Place, London W2 1PG Tel +44 (0)20 75941602 Fax +44 (0)20 75943193 f.calboli [.a.t] imperial.ac.uk f.calboli [.a.t] gmail.com </pre> Federico Calboli 2011-11-18T12:30:41 http://permalink.gmane.org/gmane.comp.lang.r.genetics/33 <pre>Dear Federico, mvtnorm is not obsolete, genetics is, and has been so for at least a year I think. The R-genetics project on Bioconductor is meant to replace it. I think most functionalities of 'genetics' are available in the packages pegas and adegenet. Cheers Thibaut. ________________________________________ From: r-sig-genetics-bounces-0bNBQ1PAWB4BXFe83j6qeQ&lt; at &gt;public.gmane.org [r-sig-genetics-bounces&lt; at &gt;r-project.org] on behalf of Federico Calboli [f.calboli-AQ/gCgVxFfnQzY9nttDBhA&lt; at &gt;public.gmane.org] Sent: 18 November 2011 11:43 To: r-sig-genetics-0bNBQ1PAWB4BXFe83j6qeQ&lt; at &gt;public.gmane.org Subject: [R-sig-genetics] package mvtnorm is obsolete Loading required package: combinat Attaching package: ‘combinat’ The following object(s) are masked from ‘package:utils’: combn Loading required package: gdata gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED. gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED. Attaching package: ‘gdata’ The following object(s) are masked from ‘package:Hmisc’: combine The following object(s) are masked from ‘package:stats’: nobs The following object(s) are masked from ‘package:utils’: object.size Loading required package: gtools Loading required package: mvtnorm NOTE: THIS PACKAGE IS NOW OBSOLETE. The R-Genetics project has developed an set of enhanced genetics packages to replace 'genetics'. Please visit the project homepage at http://rgenetics.org for informtion. Attaching package: ‘genetics’ Ok, I went on to http://rgenetics.org/trac/rgalaxy but no clear guidance is present on mvtnorm. Aside from the message, wich I am happy to ignore, is there any other thing to do/be aware of? bw F -- Federico C. F. Calboli Neuroepidemiology and Ageing Research Imperial College, St. Mary's Campus Norfolk Place, London W2 1PG Tel +44 (0)20 75941602 Fax +44 (0)20 75943193 f.calboli [.a.t] imperial.ac.uk f.calboli [.a.t] gmail.com _______________________________________________ R-sig-genetics mailing list R-sig-genetics-0bNBQ1PAWB4BXFe83j6qeQ&lt; at &gt;public.gmane.org https://stat.ethz.ch/mailman/listinfo/r-sig-genetics </pre> Jombart, Thibaut 2011-11-18T12:22:30 http://permalink.gmane.org/gmane.comp.lang.r.genetics/32 <pre>Loading required package: combinat Attaching package: ‘combinat’ The following object(s) are masked from ‘package:utils’: combn Loading required package: gdata gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED. gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED. Attaching package: ‘gdata’ The following object(s) are masked from ‘package:Hmisc’: combine The following object(s) are masked from ‘package:stats’: nobs The following object(s) are masked from ‘package:utils’: object.size Loading required package: gtools Loading required package: mvtnorm NOTE: THIS PACKAGE IS NOW OBSOLETE. The R-Genetics project has developed an set of enhanced genetics packages to replace 'genetics'. Please visit the project homepage at http://rgenetics.org for informtion. Attaching package: ‘genetics’ Ok, I went on to http://rgenetics.org/trac/rgalaxy but no clear guidance is present on mvtnorm. Aside from the message, wich I am happy to ignore, is there any other thing to do/be aware of? bw F -- Federico C. F. Calboli Neuroepidemiology and Ageing Research Imperial College, St. Mary's Campus Norfolk Place, London W2 1PG Tel +44 (0)20 75941602 Fax +44 (0)20 75943193 f.calboli [.a.t] imperial.ac.uk f.calboli [.a.t] gmail.com </pre> Federico Calboli 2011-11-18T11:43:57 http://permalink.gmane.org/gmane.comp.lang.r.genetics/31 <pre>Dear All, the new package MultiPhen is up. The latest version is 0.2, which should be available in a couple of days from a CRAN mirror near to you. MultiPhen performs genetic association tests between SNPs (one-at-a-time) and multiple phenotypes (separately or in joint model). So far it deals with SNPs, called or imputed, CNV and raw calls will be added in future releases. bw Federico -- Federico C. F. Calboli Department of Epidemiology and Biostatistics Imperial College, St. Mary's Campus Norfolk Place, London W2 1PG Tel +44 (0)20 75941602 Fax +44 (0)20 75943193 f.calboli [.a.t] imperial.ac.uk f.calboli [.a.t] gmail.com </pre> Federico Calboli 2011-07-12T16:45:45 http://permalink.gmane.org/gmane.comp.lang.r.genetics/29 <pre>Dear Marcelo, numbers of alleles per locus and heterozygosity (expected, observed) are given by the summary function of genind objects in adegenet. Global F statistics can be computed using the function fstat, and pairwise Fst using pairwise.fst. You will find more information on the adegenet website: http://adegenet.r-forge.r-project.org/ All the best, Thibaut -- ###################################### Dr Thibaut JOMBART MRC Centre for Outbreak Analysis and Modelling Department of Infectious Disease Epidemiology Imperial College - Faculty of Medicine St Mary’s Campus Norfolk Place London W2 1PG United Kingdom Tel. : 0044 (0)20 7594 3658 t.jombart-AQ/gCgVxFfnQzY9nttDBhA&lt; at &gt;public.gmane.org http://sites.google.com/site/thibautjombart/ http://adegenet.r-forge.r-project.org/ ________________________________________ From: r-sig-genetics-bounces-0bNBQ1PAWB4BXFe83j6qeQ&lt; at &gt;public.gmane.org [r-sig-genetics-bounces&lt; at &gt;r-project.org] On Behalf Of Marcelo Laia [marcelolaia-Re5JQEeQqe8AvxtiuMwx3w&lt; at &gt;public.gmane.org] Sent: 22 March 2011 12:37 To: r-sig-genetics-0bNBQ1PAWB4BXFe83j6qeQ&lt; at &gt;public.gmane.org Subject: [R-sig-genetics] Microsatellite analysis - Genetic Structure Hi, I would like to calculate genetic polymorphism for each population (mean number of alleles per locus (A), the percentage of polymorphic loci (P), the mean observed heterozygosity (HO) and the mean expected heterozygosity under Hardy-Weinberg equilibrium (HE)), and population differentiation (analyzed for polymorphic loci by F-statistics (Wright 1978)). Please, could you point me out any paper or packages that do that? Thank you very much! Marcelo _______________________________________________ R-sig-genetics mailing list R-sig-genetics-0bNBQ1PAWB4BXFe83j6qeQ&lt; at &gt;public.gmane.org https://stat.ethz.ch/mailman/listinfo/r-sig-genetics </pre> Jombart, Thibaut 2011-03-23T16:13:32 http://permalink.gmane.org/gmane.comp.lang.r.genetics/28 <pre>Hi, I would like to calculate genetic polymorphism for each population (mean number of alleles per locus (A), the percentage of polymorphic loci (P), the mean observed heterozygosity (HO) and the mean expected heterozygosity under Hardy-Weinberg equilibrium (HE)), and population differentiation (analyzed for polymorphic loci by F-statistics (Wright 1978)). Please, could you point me out any paper or packages that do that? Thank you very much! Marcelo </pre> Marcelo Laia 2011-03-22T12:37:44 http://permalink.gmane.org/gmane.comp.lang.r.genetics/27 <pre>Dear Nevil, yes, I have just implemented a pairwise Fst in adegenet a few days ago. You'll need to install the devel version from R-forge: install.packages("adegenet",repos="http://r-forge.r-project.org") Then, have a look at the function pairwise.fst. Best regards Thibaut -- ###################################### Dr Thibaut JOMBART MRC Centre for Outbreak Analysis and Modelling Department of Infectious Disease Epidemiology Imperial College - Faculty of Medicine St Mary’s Campus Norfolk Place London W2 1PG United Kingdom Tel. : 0044 (0)20 7594 3658 t.jombart-AQ/gCgVxFfnQzY9nttDBhA&lt; at &gt;public.gmane.org http://sites.google.com/site/thibautjombart/ http://adegenet.r-forge.r-project.org/ ________________________________________ From: r-sig-genetics-bounces-0bNBQ1PAWB4BXFe83j6qeQ&lt; at &gt;public.gmane.org [r-sig-genetics-bounces&lt; at &gt;r-project.org] On Behalf Of Nevil Amos [nevil.amos-sFbbPxZDHXw0n/F98K4Iww&lt; at &gt;public.gmane.org] Sent: 16 September 2010 00:48 To: r-sig-genetics-0bNBQ1PAWB4BXFe83j6qeQ&lt; at &gt;public.gmane.org Subject: [R-sig-genetics] Pairwise Fst and G'st in R Is anyone aware of functions(s) packages in R: thant caclulate pairwise Fst and or G'st between all populations in a dataset? cheers Nevil Amos _______________________________________________ R-sig-genetics mailing list R-sig-genetics-0bNBQ1PAWB4BXFe83j6qeQ&lt; at &gt;public.gmane.org https://stat.ethz.ch/mailman/listinfo/r-sig-genetics </pre> Jombart, Thibaut 2010-09-16T08:29:23 http://permalink.gmane.org/gmane.comp.lang.r.genetics/26 <pre>Is anyone aware of functions(s) packages in R: thant caclulate pairwise Fst and or G'st between all populations in a dataset? cheers Nevil Amos </pre> Nevil Amos 2010-09-15T23:48:29 http://permalink.gmane.org/gmane.comp.lang.r.genetics/25 <pre> We have some tools that I think have been put into an R package but not sent to CRAN. They implement the methods in http://onlinelibrary.wiley.com/resolve/doi/pdf?DOI=10.1002/gepi.20516 This has been used for data sets up to 16000 people x 1M SNPs. I will check to see the current status of the code -- the plan is to refactor it and combine with our analysis code for a Bioconductor package. -thomas On Sat, 11 Sep 2010, Ross wrote: Thomas Lumley Professor of Biostatistics University of Washington, Seattle _______________________________________________ R-sig-genetics mailing list R-sig-genetics-0bNBQ1PAWB4BXFe83j6qeQ&lt; at &gt;public.gmane.org https://stat.ethz.ch/mailman/listinfo/r-sig-genetics </pre> Thomas Lumley 2010-09-12T19:13:01 http://permalink.gmane.org/gmane.comp.lang.r.genetics/24 <pre>Hi Brad Work on the rgenetics tools in R has more or less come to a halt - I'm not aware of anyone working on them and I don't think many people are using them although we tried hard! I think David Clayton's package snpMatrix can handle large datasets but it's something of a struggle to fit billions of genotypes efficiently into the R memory model. For me personally, a bigger problem is enabling the Faculty and biologists I support to work reproducibly without having to worry about the technical problems of hundreds of GB of data. Galaxy really helps with those goals so I've shifted my effort to that framework. The Galaxy tools do use R and BioC under the hood where they're the best solution - but for SNP QC, Plink seems more appropriate because it has the specialized reporting we needed. On Sat, Sep 11, 2010 at 6:00 AM, &lt;r-sig-genetics-request-0bNBQ1PAWB4BXFe83j6qeQ&lt; at &gt;public.gmane.org&gt; wrote: </pre> Ross 2010-09-11T12:53:06 http://permalink.gmane.org/gmane.comp.lang.r.genetics/23 <pre>Hi Ross, Thanks for this. I take it then that the QC tools you have in Galaxy are not in any of the Bioconductor Genetics{Base,Design,Ped} packages? If not, are there plans to update the Bioconductor packages? Cheers, Brad --- Brad McNeney Statistics and Actuarial Science Simon Fraser University On 10/09/2010 11:51 AM, Ross wrote: </pre> Brad McNeney 2010-09-10T23:54:46 http://permalink.gmane.org/gmane.comp.lang.r.genetics/22 <pre>Hi, Fernando, I think there are some QC tools in David Clayton's snpMatrix package, but there's no single R package to do all the reports you need AFAIK. For comprehensive reporting, if you don't mind not using R, one option is to try the SNP/WGA tools in Galaxy - they do use R for graphics but you don't need to install anything as it all works through an ordinary web browser. Essentially, if you have your genotype and pedigree data in Plink style linkage format (separate map and ped files), the steps are something like this: 1. make yourself a new user account at the main Galaxy server (http://usegalaxy.org) so your histories are preserved between logins 2. From the analysis window, left (tool) pane, click the Get Data tool group header to expand the group, then click the 'upload file' tool. A form will appear in the center pane of your browser. 3. Change the file format (first field on the form) from Auto to "lped" format as autodetect won't work for these multi-part datatypes 4. Make the 'ped' and 'map' file upload fields point to the right map and ped files on your local machine, set the 'build' to hg18 and change the name to reflect something informative about your data then click execute. 5. After the data are uploaded (should only take a minute or two for a small file) to your history, you can select the SNP/WGA QC LD Plots tool submenu in the tool pane and then click the QC tool. Another form will open in the center panel. Your new dataset should be the only one available in the drop-down list of files to process. Change the QC job name to a meaningful name, click 'execute'. For a small dataset, the whole process should run for a few minutes but you can safely log out and log back in later - your work will all be preserved. 6. The QC tool output (in the right side history pane) has an 'eye' icon which you can click to open up the report in the center panel - you should see HWE/missingness/Mendel and all sorts of other useful plots and there are some tabular files containing summary details by marker and by sample. I'm happy to answer any questions you might have - I hope this helps get you started? There's a 'clean' tool you can use to remove markers and subjects that fall below specific thresholds for QC measures and there's a TDT tool you can use for analysis of family data. On Fri, Sep 10, 2010 at 6:00 AM, &lt;r-sig-genetics-request-0bNBQ1PAWB4BXFe83j6qeQ&lt; at &gt;public.gmane.org&gt; wrote: </pre> Ross 2010-09-10T18:51:42 http://permalink.gmane.org/gmane.comp.lang.r.genetics/21 <pre> This e-mail message may contain privileged and/or confidential information, and is intended to be received only by persons entitled to receive such information. If you have received this e-mail in error, please notify the sender immediately. Please delete it and all attachments from any servers, hard drives or any other media. Other use of this e-mail by you is strictly prohibited. All e-mails and attachments sent and received are subject to monitoring, reading and archival by Monsanto, including its subsidiaries. The recipient of this e-mail is solely responsible for checking for the presence of "Viruses" or other "Malware". Monsanto, along with its subsidiaries, accepts no liability for any damage caused by any such code transmitted by or accompanying this e-mail or any attachment. The information contained in this email may be subject to the export control laws and regulations of the United States, potentially including but not limited to the Export Administration Regulations ("EAR") and sanctions regulations issued by the U.S. Department of Treasury, Office of Foreign Asset Controls (“OFAC”). As a recipient of this information you are obligated to comply with all applicable U.S. export laws and regulations. _______________________________________________ R-sig-genetics mailing list R-sig-genetics-0bNBQ1PAWB4BXFe83j6qeQ&lt; at &gt;public.gmane.org https://stat.ethz.ch/mailman/listinfo/r-sig-genetics </pre> GRIGNOLA, FERNANDO E [AG/1000] 2010-09-09T15:54:23 http://permalink.gmane.org/gmane.comp.lang.r.genetics/20 <pre></pre> Gloria Rocio Bautista 2010-09-07T18:38:24 http://permalink.gmane.org/gmane.comp.lang.r.genetics/19 <pre></pre> Gloria Rocio Bautista 2010-09-07T18:37:01 http://permalink.gmane.org/gmane.comp.lang.r.genetics/18 <pre>ah - the rgGRR Galaxy code uses python/weave C code and is limited to biallelics so easy to estimate alleles shared as 0,1 or 2 - interesting to see how that will work for microsatellites. Probably not too hard to write R code to do the calculations but I don't know of any existing routines.. On Mon, Jun 28, 2010 at 10:04 PM, Nevil Amos &lt;nevil.amos-Re5JQEeQqe8AvxtiuMwx3w&lt; at &gt;public.gmane.org&gt; wrote: </pre> Ross 2010-06-28T23:22:20 http://permalink.gmane.org/gmane.comp.lang.r.genetics/17 <pre>Do any of the genetics related packages allow calcualtion of individual relatedness values? such as that in Queller, D.C. and Goodnight, K.F. 1989. Estimation of genetic relatedness using allozyme data. Evolution 43:258-275.? cheers Nevil Amos [[alternative HTML version deleted]] </pre> Nevil Amos 2010-06-26T17:48:33 http://permalink.gmane.org/gmane.comp.lang.r.genetics/16 <pre> You could format and prepare your data within R, output to a text file and then make a system call to your external program(s) from within R to perform the calculations before reading them back into R for summarising and presenting. A bit of work I'd imagine, but I'd guess it has the potential of being developed into a package for subsequent use by yourself and others. Also whilst typing that I remembered that Shaun Purcell's Plink (see http://pngu.mgh.harvard.edu/~purcell/plink/) has some integration with R, although its mainly geared towards analysis of SNPs and CNVs (but given that it can handle multi-marker haplotypes it should be capable of handling multi-allelic microsatellites). Regards Neil </pre> Neil Shephard 2010-06-28T13:00:16 Search the mailing list at Gmane query http://search.gmane.org/?group=$group=gmane.comp.lang.r.genetics