Question: Add gene annotation/information to CNV plot in R
0
gravatar for Floris Brenk
10 months ago by
Floris Brenk850
USA
Floris Brenk850 wrote:

Hi all,

Im have a few interesting (genotyping) CNVs and now I want to plot them using the B allele frequency and LogR ratio. There are already several topics about this for example here, but ideally I am more looking for something like pennCNV plots but then with gene annotation on the x-axis (example below). Because when doing it genome-wide for random genes is it a bit time consuming to look up the actual genes and manually add these in R. Any ideas?

example

plot cnv R • 732 views
ADD COMMENTlink modified 10 months ago by cmdcolin870 • written 10 months ago by Floris Brenk850
0
gravatar for cmdcolin
10 months ago by
cmdcolin870
United States
cmdcolin870 wrote:

In some cases converting your data to a genome browser and then screenshotting the genome browser can be beneficial for getting such genomic contexts.

The embedded link also recommends something called genomegraphs also which helps for R graphics

A final alternative you could look into is adding annotations onto an existing plot. Annotating ggplots is pretty pleasant (you can annotate using the same coordinate space as the data that you are plotting) so you can have http://ggplot2.tidyverse.org/reference/annotate.html. Using base graphics it could be a little bit different.

Reading gene annotation data such as GFF is a tabular format, which R can load pretty easily. Just draw a box covering the gene regions (rows in a gff that have a gene line), or you can also try and draw the intron-exon boundaries if you feel this is important too

ADD COMMENTlink modified 10 months ago • written 10 months ago by cmdcolin870
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