Question: Is there any way to set bsseq object as 'smoothed'?
0
2.9 years ago by
biohack920 wrote:

I have bsseq objects for that have already been smoothed, and I want to plot the BSmooth methylation estimates using the plotManyRegions function. I had to process each chromosome separately and combine them into a single bsseq object, but I can't use the function as the bsseq object has to have been smoothed by the BSmooth function.

> plotManyRegions(plus, d, extend=2000, addRegions=d)
Error in getMeth(BSseq, type = "smooth") :
'type=smooth' requires the object to have been smoothed.

bsseq bisulfite • 625 views
modified 2.9 years ago • written 2.9 years ago by biohack920
Answer: Is there any way to set bsseq object as 'smoothed'?
0
2.9 years ago by
United States
Kasper Daniel Hansen6.4k wrote:
Are you sure when you combine data from different chromosomes that it still contains the smoothing estimates? I think my code for combining bsseq objects will drop the smoothing (which in your case it arguably shouldn't, but I think it will). One way to fix this quickly is to just plot the stuff using plotManyRegions on each chromosome. You'll be happy to hear that we are working on more scalable code for this, since we now have experiments with a substantial number of samples, but we don't have anything ready for common usage (and it will be a while before we have). On Fri, Apr 22, 2016 at 12:26 AM, biohack92 [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User biohack92 <https: support.bioconductor.org="" u="" 10159=""/> wrote Question: > Is there any way to set bsseq object as 'smoothed'? > <https: support.bioconductor.org="" p="" 81150=""/>: > > I have bsseq objects for that have already been smoothed, and I want to > plot the BSmooth methylation estimates using the plotManyRegions function. > I had to process each chromosome separately and combine them into a single > bsseq object, but I can't use the function as the bsseq object has to have > been smoothed by the BSmooth function. > > Error in getMeth(BSseq, type = "smooth") : > 'type=smooth' requires the object to have been smoothed. > > Appreciate your help. > > > > ------------------------------ > > Post tags: bsseq, bisulfite > > You may reply via email or visit Is there any way to set bsseq object as 'smoothed'? >
Answer: Is there any way to set bsseq object as 'smoothed'?
0
2.9 years ago by
biohack920 wrote:

Hi Kasper,

Thanks for the quick reply. Before combining the individual bsseq objects, all objects have the smoothed designation.

I should clarify that I was able to generate the plots using the plotManyRegions function after splitting by chromosome. Additional filtering post-smoothing reduced the number of DMRs, so rather than sifting through plots in each file/chromosome to grab the plots in the order of ranking of the DMRs, I hoped to combine bsseq objects and use the ranked DMRs for the plotManyRegions.

I'll recheck the script and I hope it's a mistake I made somewhere. Appreciate the update and I look forward to an update!