Question: "three genes" exemple in genoplotR
1
gravatar for buthercup_ch
5.1 years ago by
buthercup_ch30
Japan
buthercup_ch30 wrote:

Hello everyone,

I'm starting to use R/Bioconductor, and the package genoplotR in order to visualize the alingemnt of a set of gene operons in several bacterial strains.    

Before going my data, I'm trying the "getting started" vignette coming with the package, and succeed in getting the plot corresponding to the example "three genes"... but... I don't have that much experience using R and am not able to visualize how they look the data it selves.

I mean, the first line of the code in the example is:  

> data("three_genes")

I want to see those data. How can I do it?

Thank you very much in advance 

 

 

gene R genome • 1.8k views
ADD COMMENTlink modified 5.1 years ago • written 5.1 years ago by buthercup_ch30

I do have the same question and I did, in the past worked with R. I would really like to see how the "three_genes" dataset looks like, I tried several things but for some reason is not an object.... did you find your answer?...

ADD REPLYlink written 3.4 years ago by lay_050
1
gravatar for komal.rathi
5.1 years ago by
komal.rathi3.5k
Children's Hospital of Philadelphia, Philadelphia, PA
komal.rathi3.5k wrote:

I think you should read the full tutorial properly. Loading the dataset 'three_genes' will automatically load two lists 'comparisons' and 'dna_segs'. That's what you will be working with. 

ADD COMMENTlink modified 5.1 years ago • written 5.1 years ago by komal.rathi3.5k
0
gravatar for RamRS
5.1 years ago by
RamRS26k
Houston, TX
RamRS26k wrote:

Have you tried view(three_genes)? I hope you're using RStudio, makes learning easier.

ADD COMMENTlink written 5.1 years ago by RamRS26k
0
gravatar for buthercup_ch
5.1 years ago by
buthercup_ch30
Japan
buthercup_ch30 wrote:

> View(three_genes)
Error in View : object 'three_genes' not found

ADD COMMENTlink written 5.1 years ago by buthercup_ch30
0
gravatar for buthercup_ch
5.1 years ago by
buthercup_ch30
Japan
buthercup_ch30 wrote:

Dear komal.rathi, thank you for your answer.

I've read the full tutorial... I know the data are downloaded with the package, but I'm not able to see where they are. At least they are not listed in the "environment" window, upper right window in RStudio.

This question might sound stupid for you, but as I already said, I'm less than beginner and I'm getting really frustrated with this.

I really would like to get more into bioinformatics, but honestly, I don't find very easy to follow the "user's manual"... as they always neglect the very basics. And again..., I'm not able to find a good tutorial explaining the very basics...

Well, it might be that I am completely incapable.

 

ADD COMMENTlink written 5.1 years ago by buthercup_ch30

Umm, I did not mean to offend you. Anyway, so are you referring to this manual? It seems pretty straightforward to me. You need to go one step at a time. If you are a beginner, genoPlotR is not really a good place to start with. Why don't you start with the basics and then get to this package. 

ADD REPLYlink written 5.1 years ago by komal.rathi3.5k

Sorry... umm... I've been slightly rude. I apologize for that.

Is just I am a "wet" person, with no formation in informatics or programming at all... I am actually using other kind of "user friendly" bioinformatics tools to get the alignment of my genes set and then drawing by hand using powerpoint. But I would like to use some "more scientific tool" than powerpoint to make the plotting.  I have struggled with R and all different packages for RNA-Seq analysis while working in a different project, all by myself and with no bioinformatic assistance, and finally quit because of my lack of the very basics, but genoplotR seemed much more easy to use. I

Again, I haven't been able to find a proper manual describing the very basics... something friendly for non-bioinformaticians. If you know any tutorial of this kind, please, let me know about it. I would really appreciate some help.

ADD REPLYlink written 5.1 years ago by buthercup_ch30

Komal is right. We have no idea about your background and usually assume that you are good with the basics of R when you start working on specialized packages. Like she said, start from the basics. And observe the outcome of every step.

For example, when you ran the first command on Rstudio, the objects window will show you the objects it imported. If you started with the basics, the introduction to RStudio would have made you aware of this and you'd never have this confusion in the first place.

And remember, this may sound a bit too frank, but self pity will not work in your favor in online communities.

ADD REPLYlink written 5.1 years ago by RamRS26k

Thank you RamRS for your frankness. I was not trying to show self-pityness, just to point out in a clear way the level of  my skills. I'm sorry if this community may be "hurt" by this.

I've started to write a code by using my own data, but still cannot see how the "three_genes" file look like or where is it located.

 

ADD REPLYlink written 5.1 years ago by buthercup_ch30

Good that your intention was just to apprise us of your skill levels. I apologize for any misunderstanding - online communication is subject to a lot of misinterpretation.

Think of the code this way: the three_genes is like a peanut with a shell. When you load the peanut, you crack it open to reveal the two kernels within, which are the comparisons and names datasets.

The three_genes is just the container name of a data set that is packed with the genoplotR package by default. When it is loaded, the container is unwrapped and it reveals the actual variables within.

ADD REPLYlink written 5.1 years ago by RamRS26k
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