Obtaining an NChannelSet from the IDATs is not hard (IIRC, minfi will
happily do this as well):

R> NCh = methylumi:::DFsToNChannelSet(IDATsToDFs(barcodes, idatPath='.'))

But there don't seem to be any coercion methods for turning it into an
RGChannelSet:

R> library(minfi)
R> RGset <- as(NCh, 'RGChannelSet')
Error in as(NCh, "RGChannelSet") :
  no method or default for coercing "NChannelSet" to "RGChannelSet"

I would think that coercing a MethyLumiSet to a MethylSet would actually be
more productive for using dmr/dmpFinder, etc.   If it is not obnoxious I
will look into adding a coercion for MethyLumiM/MethyLumiSets to
MethylSets; I recently added one for coercing a MethyLumiSet into a GenoSet
(nice plotting and subsetting functions) and a SummarizedExperiment (same
reasons).



On Fri, Feb 17, 2012 at 11:14 AM, Aaron Mackey <amackey@virginia.edu> wrote:

> I'm using the methylumIDAT() function from the methylumi package to read
> data directly from raw .idat files (it was not clear to me whether this
> functionality exists in the minfi package); but I'd like to be able to use
> this object in minfi functions (e.g. controlStripPlot, dmpFinder, etc.),
> but minfi expects RGChannelSet objects, not MethylLumiSet objects.  Is
> there a way to cast one into the other?
>
>
> Thanks again,
> -Aaron
>
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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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