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://comments.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://comments.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</pre> Ilaria Coscia 2012-01-11T15:50:53 http://comments.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 </pre> Federico Calboli 2011-11-18T11:43:57 http://comments.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://comments.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://comments.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://comments.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://comments.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 reg</pre> GRIGNOLA, FERNANDO E [AG/1000] 2010-09-09T15:54:23 http://comments.gmane.org/gmane.comp.lang.r.genetics/20 <pre></pre> Gloria Rocio Bautista 2010-09-07T18:38:24 http://comments.gmane.org/gmane.comp.lang.r.genetics/19 <pre></pre> Gloria Rocio Bautista 2010-09-07T18:37:01 http://comments.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://comments.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 http://comments.gmane.org/gmane.comp.lang.r.genetics/13 <pre>Is the calculation of pairwise relateness eg. Queller and Goodnight 1989 avaiable in any R: package? cheers </pre> Nevil Amos (Sci 2010-06-27T17:50:06 http://comments.gmane.org/gmane.comp.lang.r.genetics/12 <pre>Hi all, here is the function to calculate Nei-Li (1979) distance (or dissimilarity) for a binary matrix where columns are species and rows are alleles. It is a modification of "jaccard" function in package prabclus by Christian Hennig and Bernhard Hausdorf. ######################################## neidist&lt;-function (regmat) { nart &lt;- ncol(regmat) jdist &lt;- rep(0, nart * nart) dim(jdist) &lt;- c(nart, nart) reg.col.sum &lt;- apply(regmat, 2, sum) reg.aggrement &lt;- t(regmat) %*% regmat nedist &lt;- 1 - (reg.aggrement+reg.aggrement)/((reg.col.sum - t(t(reg.aggrement) - reg.col.sum))+reg.aggrement) nedist } ############################################### Useful in AFLP or other dominant (0-1 response) markers analysis Fiorello Toneatto </pre> gmail 2009-09-22T14:51:11 Search the mailing list at Gmane query http://search.gmane.org/?group=$group=gmane.comp.lang.r.genetics