DMRseq smoothed values
1
0
Entering edit mode
swebb1 • 0
@swebb1-11141
Last seen 4.3 years ago

Is there a way to export the smoothed methylation values from DMRseq across the entire genome? I'd like to store them inĀ  bigWig file to view in a genome browser.

dmrseq • 571 views
ADD COMMENT
0
Entering edit mode
keegan ▴ 60
@keegan-11987
Last seen 20 months ago
Vancouver, BC, Canada

Hi swebb1,

dmrseq does not compute smoothed methylation values. Instead, it smooths methylation differences with respect to the covariate of interest. These smoothed methylation differences are not stored. If obtaining these values would be useful, I would consider adding an option to store/export them. If you are interested in obtaining smoothed methylation values, you can obtain these via the BSmooth() function in the bsseq package.

Best,
Keegan

ADD COMMENT
0
Entering edit mode

Hi Keegan,

I was essentially looking for the lines plotted in plotDMRs() function but I assume these are just created on the fly. I will run BSmooth for the entire genome for now, thanks for your help.

ADD REPLY
0
Entering edit mode

Ah, yes the smoothed lines generated in plotDMRs() for visualization purposes are generated on the fly, so they are not created for the entire genome. BSmooth() will compute smoothed values for the whole BSseq object, however. Hope that helps!

ADD REPLY

Login before adding your answer.

Traffic: 462 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6