From lionel.guy at imbim.uu.se Thu Oct 27 09:58:45 2016 From: lionel.guy at imbim.uu.se (Lionel Guy) Date: Thu, 27 Oct 2016 07:58:45 +0000 Subject: [genoPlotR-help] genoplotR In-Reply-To: References: Message-ID: Dear Ingrid Meyer, You?ll find some info in section 4 of the ?getting started? page (http://genoplotr.r-forge.r-project.org/vignette.php). Typically, genomes/chromosomes/plasmids are formatted under EMBL or Genbank files. I assume you are familiar with these formats, which are offered by both NCBI and EMBL. Reading functions in genoPlotR are read_dna_seg_from_genbank and read_dna_seg_from_embl, respectively. For comparisons, the tabular output of blast (-outfmt 6) can be read directly read (read_comparison_from_blast). Alternatively, you can create your own tab files, which should contain at least the columns start1, end1, start2, end2. More info in the specific help pages (type ?read_comparison_from_blast in R). Hope that helps, Lionel > On 26 Oct 2016, at 14:25 , Ingrid Eileen Meyer Cifuentes wrote: > > Dear Mr. Guy, > > I am Ingrid Meyer from Germany, currently doing my PhD at the Helmholtz Centre-UFZ. I am contacting you in order to ask about the package you developed "genoplotR". Unfortunately, I am not so good with R therefore I have had some difficulties trying this program. I have read all the online manuals for the program and looked for forums as well.. unfortunately there is not much more information for it. Overall I understand the codes, but is not clear for me how the data I want to analyze should be structured or how should look like. Is there any course offered by you or colleagues that I could attend to? Or any video tutorial I could follow? I would appreciate enormously if you could give me a hand. > > Thank you in advance, > > Ingrid Meyer C. > > -- > Ingrid Meyer C. > > Doktorand | PhD student > Department Umweltbiotechnologie (UBT) > Department Environmental Biotechnology (UBT) > > Helmholtz Zentrum f?r Umweltforschung GmbH - UFZ > Helmholtz Centre for Environmental Research GmbH - UFZ > > Permoserstra?e 15 | 04318 Leipzig | Germany > Telefon +49 341 235 1757 > ingrid-eileen.meyer-cifuentes at ufz.de -- Lionel Guy Department for Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden phone: +46 18 471 4246; mobile +46 73 976 0618; postal address: Box 582, SE-751 23 Uppsala; visiting address: BMC D7:304c, Husargatan 3, SE-752 37 Uppsala lionel.guy at imbim.uu.se