[genoPlotR-help] genoplotR

[Lionel Guy]

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 <ingrid-eileen.meyer-cifuentes at ufz.de> 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 für Umweltforschung GmbH - UFZ
> Helmholtz Centre for Environmental Research GmbH - UFZ
> 
> Permoserstraße 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