Closed DengEr-1993 closed 4 months ago
Hi @DengEr-1993,
You can add gene tracks to the plot using the annoTrack
argument in plotDMRs
(you pass the output of getAnnot
) - see this section of the vignette for example. Note that if there are no genes in the region plotted, then no gene tracks will be shown.
Best, Keegan (she/her/hers)
@kdkorthauer Thank you for you answer. You may not understand my question. I know how to add the gene information through the annoTrack
parameter and it works perfect.
But I want to show one gene that I am interested in. For example, the gene SAMD11 (I select it randomly here), if it has significance after dmrseq
, and then I want to see methylation on this gene. So how should I do to focus this region ?Thank you.
The purpose of the function is really focused on visualizing DMRs. To do what you are proposing, you would need to construct that region yourself (e.g. a region containing SAMD11) and pass it to the plotting function. Or, select the DMR(s) that overlap a region containing your gene of interest using GenomicRanges
functions, and then pass that to the plotting function. Hope that helps!
Best, Keegan
Sorry @kdkorthauer
It is my second question.
For example, I want to show specific gene symbol and its CpG methylation points or regions.
So how can I specify this gene by annoTrack, regions&blocks or even the bsseq result ?
Or should I do this procedure manually ? ##############
Thanks!