the obvious thing to do would be to use minfi's mapToGenome function:

require(minfi)
require(minfiData)
dat <- preprocessIllumina(RGsetEx, bg.correct=T, normalize="controls")
mapped <- mapToGenome(dat)

and then coerce the resulting SummarizedExperiment to a genoset:

mgset <- as(mapped, 'MethyGenoSet')
## Error in as(mapped, "MethyGenoSet") :
##  no method or default for coercing "GenomicMethylSet" to "MethyGenoSet"

That's a shame, because I added coercions in methylumi-dev that go from
MethyLumiSet/MethyLumiM objects to SummarizedExperiments (GenomicMethylSet
is just a subclass of SummarizedExperiment), and it would make sense to
have a coercion to/from genoset-derived objects and SummarizedExperiment
objects.

All of these things serve a common purpose: to map loci to the genome.
The only thing that's different is the precise mechanism, and I don't think
that's really a showstopper.  All of the packages that deal with DNA
methylation (methylumi, methyAnalysis, minfi, bsseq, QuasR) eventually
return an object that reflects how much evidence there is for methylation
at a given genomic position (or, in some cases, a range of positions -- a
similar basic problem).

I'll look into how annoying (or not) it would be to write this plumbing,
mostly since I use all of the above on a regular basis, and have a small
stack of partially-responded-to emails from this list that could be
addressed thusly.

Best,

--t



On Thu, Feb 28, 2013 at 3:32 AM, Zilbauer Matthias
<mz304@medschl.cam.ac.uk>wrote:

> Dear all,
> I am using the minfi package to pre-process my K450 methylation data as
> well as to
> test for differentially methylated probes/positions (dmps). However, I
> would also like to identify
> differentially methylated regions (dmrs) and have tried the MethyAnalysis
> package for this.
>
> Does anyone know how to use bumphunter for minfi data or alternatively how
> to
> coerce an RGset object into a GenoSet object?
>
> Any suggestions and help would be much appreciated.
> Many thanks in advance
>
> Matt
>
>
>
>
>
> ====================================
> Matthias Zilbauer MD PhD MRCPCH
> Clinical lecturer in Paediatric Gastroenterology
> Department of Paediatric Gastroenterology
> Box 267, Addenbrooke's Hospital
> Hills Road, Cambridge, CB2 0QQ
>
> Lab:
> Adult and Paediatric Gastroenterology Research Unit
> Level 7, Addenbrooke's Hospital
> Hills Road, Cambridge, CB2 0QQ
>
>
>
>
>
>
>         [[alternative HTML version deleted]]
>
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>



-- 
*A model is a lie that helps you see the truth.*
*
*
Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>

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