convert between MethylLumiSet (methylumi) and RGChannelSet (minfi)
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Aaron Mackey ▴ 170
@aaron-mackey-4358
Last seen 9.6 years ago
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 [[alternative HTML version deleted]]
methylumi minfi methylumi minfi • 2.8k views
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Tim Triche ★ 4.2k
@tim-triche-3561
Last seen 3.5 years ago
United States
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 > > [[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]]
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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 >> >> ? ? ? ?[[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at 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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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