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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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- *A model is a lie that helps you see the truth.* * * Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> [[alternative HTML version deleted]]