It’s all working now. Thanks, Thibaut.
Regards, Rav On 2 Sep 2016, at 10:24, Thibaut Jombart <[email protected]<mailto:[email protected]>> wrote: Hi there, Please check carefully the error msg. Here the problem is stated clearly. You either need to provide the group factor as argument to dapc, or to attach it to the object - pop(x) <- ... Cheers Thibaut On 2 Sep 2016 09:51, "Bhuller, Ravneet" <[email protected]<mailto:[email protected]>> wrote: Hello Thibaut, The genind object is of size 8.9 Mb. Yesterday, when I tried find.clusters in the Rmarkdown document, it did not ask for any input. I wanted to know how many components to retain to run DAPC. However, today, when I tried find.clusters in R (without Rmarkdown), it worked absolutely fine. But another problem is that pop function is giving an error. Attached is the screenshot. My data is DNA multiple-sequence-alignment FASTA files of 357 genes, which are concatenated. Each file has same 220 bacterial strains. And my meta data includes 220 strains distributed into 19 serovars (integers). Is my meta data in the correct required form? <DAPC ERROR.png> Kind regards, Rav On 1 Sep 2016, at 16:17, Thibaut Jombart <[email protected]<mailto:[email protected]>> wrote: Hi, what is the size of the dataset? Are you sure it did not display a graph of cumulative variance and waits for your input? As you specified it, the function is interactive and will wait on your input before giving results. Best Thibaut -- Dr Thibaut Jombart Lecturer, Department of Infectious Disease Epidemiology Imperial College London https://sites.google.com/site/thibautjombart/ https://github.com/thibautjombart Twitter: @TeebzR <https://twitter.com/TeebzR> On 1 September 2016 at 00:33, Graham Reynolds <[email protected]<mailto:[email protected]>> wrote: Hi Rav, if you have multiple cores on your CPU you can distribute the task among them, which really speeds it up. That might at least let you see whether it is a problem with the dataset. grp <-find.clusters(app, max.n.clust=n, parallel = "multicore", ncpus = 4) You might need to install the Parallel package Cheers R. Graham Reynolds, Ph.D. Assistant Professor of Biology University of North Carolina Asheville www.caribbeanboas.org<http://www.caribbeanboas.org/> *From:* R-sig-genetics <[email protected]<mailto:[email protected]>> on behalf of Bhuller, Ravneet <[email protected]<mailto:[email protected]>> *Sent:* Wednesday, August 31, 2016 5:39 AM *To:* [email protected]<mailto:[email protected]> *Subject:* [R-sig-genetics] Query regarding DAPC using ADEGENT in R Dear All, I am trying to do DAPC on my genind object (app) using ADEGENET in R. But when I run the following command: grp <- find.clusters(app) it is processing continuously for more than 2 hours but not producing any output. Any guidance will be very much appreciated. Regards, Rav [[alternative HTML version deleted]] _______________________________________________ R-sig-genetics mailing list [email protected]<mailto:[email protected]> https://stat.ethz.ch/mailman/listinfo/r-sig-genetics R-sig-genetics Info Page - stat.ethz.ch<http://stat.ethz.ch/> <https://stat.ethz.ch/mailman/listinfo/r-sig-genetics> stat.ethz.ch<http://stat.ethz.ch/> The R-sig-genetics mailing list is devoted to friendly, insightful, exciting discussions on genetic data analysis using the R software. Covered topics include: [[alternative HTML version deleted]] _______________________________________________ R-sig-genetics mailing list [email protected]<mailto:[email protected]> https://stat.ethz.ch/mailman/listinfo/r-sig-genetics [[alternative HTML version deleted]] _______________________________________________ R-sig-genetics mailing list [email protected]<mailto:[email protected]> https://stat.ethz.ch/mailman/listinfo/r-sig-genetics [[alternative HTML version deleted]] _______________________________________________ R-sig-genetics mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-genetics
