[BioC] plot methylation figure for end analysis

[Alex Gutteridge]

On 12.09.2013 08:25, Gia [guest] wrote:
> Hi,
> I would like to ask if anyone experienced with creating figures from
> BS-Seq methylation data for end analysis of genes (or any genomic
> features), like what was presented in the following link:
> http://www.nature.com/ng/journal/v39/n1/fig_tab/ng1929_F4.html
> It would be appreciate if you can show how to create this kind of
> figures using any Bioconductor packages.
> Cheers,
>
>  -- output of sessionInfo():
>
> None
>
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I've only skimmed through that paper but that figure isn't showing 
BS-Seq data as far as I can see - it's showing the results of an array / 
IP based approach to methylation quantitation. BSmooth is one of the 
best packages I've found for manipulating BS-Seq data. If you get your 
data in there you could derive analogous statistics (i.e. methylation 
levels) pretty easily. Then any of the base plotting functions will give 
you similar graphs.

-- 
Alex Gutteridge