[BioC] convert between MethylLumiSet (methylumi) and RGChannelSet (minfi)

[Kasper Daniel Hansen]

The main input file format to minfi is IDAT files, see read.450k.exp
as well as the vignette

On Fri, Feb 17, 2012 at 8:40 PM, Tim Triche, Jr. <tim.triche at gmail.com> wrote:
> 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 at 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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>>
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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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>
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