ROH-script for graphical visualization in R

Question

[safiradrak]

Hi guys, do you know how can I get a graphical visualisation of ROH on each chromosome in R? I have a dog genotyping data - 140000 SNPs and I would like to find out how is the ROH situation in every individual I have (so far 48). I have figured out how to calculate ROH in PLINK but now I am lost...I am a newbie in this so I will be happy for every advice.

Thank you,

Silvie

Answer 1

[adily]

Hello,

I'm looking for exactly the same solution... Did you find out how to visualize ROH on each chromosome in R?

Thank you in advance,

Adily

[bernatgel]

You should be able to plot the ROH using karyoploteR. You can find information on how to use it on the vignette and a tutorial and some more complex examples with step by step instructions at [https://bernatgel.github.io/karyoploter_tutorial/].

It might even automatically read the output from plink with the toGranges function. If it does not work, you can give me a few lines from the file and I can try to guide you.

[adily]

Thank you very much for your recommendation! My result was perfect.

Do you have any idea for visualization tool of specific transcript of gene? I want to show the exons, domains and some variants.

Thanks again! Adily

[bernatgel]

Hi adily,

Happy karyoploteR worked for you.

For gene plotting I'm developing a new package, genoploteR, based on karyoploteR, but it's not yet finished. You can take a look at it at [https://github.com/bernatgel/genoploteR]. It can currently plot the gene (with tuneable intron compression) and a few type of data can be plotted on them. However there's not yet anything automatic for domains or mutation frequency (it's planned, not yet done). You can take a look at it and see if it works for you. Another option, if you are ok with your plot having whole introns (usually not whats expected) you can use "kpPlotGenes" or "kpPlotTranscripts". These are not yet incorporated to the tutorial, but work quite well.