Question: display of chromosomes (on the linear scale) and translocations
gravatar for Bogdan
11 months ago by
Palo Alto, CA, USA
Bogdan560 wrote:

Dear all,

please would you advise if there is any package in BioC/R that could help with the following data visualization : 

1 -- we have a set of SNV, CNV, SV from cancer samples

2 -- we would like to display the SNV and CNV along the chromosomes (on the linear scale, ie. HORIZONTALLY)

3 -- we would like to display the SV, especially TRANSLOCATIONS, as VERTICAL LINES connecting the breakpoints on the chromosomes that are represented HORIZONTALLY

thank you very much,

-- bogdan





ADD COMMENTlink modified 11 months ago • written 11 months ago by Bogdan560

On the same line of thought,  I believe that I could adapt the functionality of some R packages that display the synteny regions across multiple species (here please see an example Figure 1 from ),

In my case, instead of distinct species, I will just show distinct chromosomes connected by translocations, although I have not found yet a R/BioC package that does this display.  

If anyone has any suggestions, please let me know.

thanks a lot, 

-- bogdan


ADD REPLYlink modified 11 months ago • written 11 months ago by Bogdan560
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 353 users visited in the last hour