Right, my original intent was simply to coerce the SummarizedExperiment-based containers from methylumi and minfi into a genoset for Pan's package. That reminds me, I need to update the documentation for 450kProbe to note that it is essentially obsolete, since both methylumi and minfi can emit SummarizedExperiments. The only mop-up now is for me to send in a few minfi patches for processing. The innards of minfi are tidier than... Others. --t On Mar 12, 2013, at 6:57 AM, Kasper Daniel Hansen <kasperdanielhansen at="" gmail.com=""> wrote: > Lavina, > > I don't really have time to really look into all of this, but note the > function mapToGenome which associates a MethylSet with genomic > coordinates. So you can do > > gmSet = mapToGenome(mSet) > > and now you have > > granges(gmSet) # locations > getMeth(gmSet) # methylation channel > > etc. Note that the transformation is non-invertible because a few > CpGs have no associated genomic locations and they are dropped (well, > you can use drop=FALSE). > > Kasper > > On Mon, Mar 11, 2013 at 5:13 PM, Lavinia Gordon > <lavinia.gordon at="" mcri.edu.au=""> wrote: >> Argh!, thanks Martin, sorry about that. >> >> So in that case I think I've worked out a (rather ugly) way to force minfi data into a MethyGenoSet object for use within the package methyAnalysis: >> >> Library(minfi) >> # mset is minfi object, e.g. used in dmpFinder code >> myexprs <- getM(mSet) >> mymeth <- getMeth(mSet) >> myunmeth <- getUnmeth(mSet) >> >> # using Tim Triches helpful code, thanks! >> library(IlluminaHumanMethylation450kprobe) >> data(IlluminaHumanMethylation450kprobe) >> library(GenomicRanges) >> chs = levels(IlluminaHumanMethylation450kprobe$chr) >> names(chs) = paste('chr',chs,sep='') >> CpGs.450k = with(IlluminaHumanMethylation450kprobe, >> GRanges(paste('chr',chr,sep=''), >> IRanges(start=site, width=2, names=Probe_ID), >> strand=strand)) >> >> CpGs.450k.df <- as.data.frame(CpGs.450k) >> >> mylocData <- RangedData(ranges=IRanges(start=CpGs.450k.df$start, end=CpGs.450k.df$end, names=row.names(CpGs.450k.df)), space=CpGs.450k.df$seqnames) >> >> mymethy.obj <- new("MethyGenoSet", locData=mylocData, assayData=assayDataNew(exprs=new("matrix"), methylated=new("matrix"), unmethylated=new("matrix"), detection=new("matrix"))) >> >> # make sure the CpG ids in mylocData agree with what is in CpGs.450k.df >> >> exprs(mymethy.obj) <- myexprs >> methylated(mymethy.obj) <- mymeth >> unmethylated(mymethy.obj) <- myunmeth >> # had to add this afterwards >> >> methyGenoSet.sm <- smoothMethyData(mymethy.obj, winSize = 250) >> >> I haven't run through all of the MethyAnalysis functions so the MethyGenoSet object may need more information added to it, in other slots, for it to work properly. >> >> >> Lavinia Gordon >> Senior Research Officer >> Quantitative Sciences Core, Bioinformatics >> >> Murdoch Childrens Research Institute >> The Royal Children's Hospital >> Flemington Road Parkville Victoria 3052 Australia >> T 03 8341 6221 >> www.mcri.edu.au >> >> >> -----Original Message----- >> From: Martin Morgan [mailto:mtmorgan at fhcrc.org] >> Sent: Saturday, 9 March 2013 1:49 AM >> To: Lavinia Gordon >> Cc: bioconductor at r-project.org; dupan at gmal.com >> Subject: Re: [BioC] methyAnalysis - changes to GenoSet >> >> On 03/07/2013 08:23 PM, Lavinia Gordon wrote: >>> Dear Bioc users, >>> I have just tried the example code supplied with the package methyAnalysis and am getting an error: >>> >>>> ################################################### >>>> ### code chunk number 3: Slide-window smoothing of the DNA >>>> methylation data ################################################### >>>> methyGenoSet.sm <- smoothMethyData(exampleMethyGenoSet, winSize = >>>> 250) >>> Smoothing Chromosome 21 ... >>> >>> Note: Method with signature ?GenoSet#character#ANY#ANY? chosen for >>> function ?[?, target signature ?MethyGenoSet#character#character#missing?. >>> "MethyGenoSet#ANY#ANY#ANY" would also be valid Warning message: >>> The ranges method on a GenoSet is depricated. Please use space(locData(x)) or seqnames(locData(x)) as appropriate for RangedData or GRanges. >>>> methyGenoset.sm >>> Error: object 'methyGenoset.sm' not found >> >> typo -- methyGenoSet.sm >> >> Martin >> >>>> sessionInfo() >>> R version 2.15.2 (2012-10-26) >>> Platform: x86_64-redhat-linux-gnu (64-bit) >>> >>> locale: >>> [1] LC_CTYPE=en_US.UTF-8 >>> [2] LC_NUMERIC=C >>> [3] LC_TIME=en_US.UTF-8 >>> [4] LC_COLLATE=en_US.UTF-8 >>> [5] LC_MONETARY=en_US.UTF-8 >>> [6] LC_MESSAGES=en_US.UTF-8 >>> [7] LC_PAPER=C >>> [8] LC_NAME=C >>> [9] LC_ADDRESS=C >>> [10] LC_TELEPHONE=C >>> [11] LC_MEASUREMENT=en_US.UTF-8 >>> [12] LC_IDENTIFICATION=C >>> >>> attached base packages: >>> [1] grid stats graphics grDevices >>> [5] utils datasets methods base >>> >>> other attached packages: >>> [1] methyAnalysis_1.0.0 org.Hs.eg.db_2.8.0 >>> [3] RSQLite_0.11.2 DBI_0.2-5 >>> [5] AnnotationDbi_1.20.5 Biobase_2.18.0 >>> [7] IRanges_1.16.6 BiocGenerics_0.4.0 >>> >>> loaded via a namespace (and not attached): >>> [1] affy_1.36.1 affyio_1.26.0 >>> [3] annotate_1.36.0 BiocInstaller_1.8.3 >>> [5] biomaRt_2.14.0 Biostrings_2.26.3 >>> [7] biovizBase_1.6.2 bitops_1.0-5 >>> [9] BSgenome_1.26.1 cluster_1.14.3 >>> [11] colorspace_1.2-1 dichromat_2.0-0 >>> [13] genefilter_1.40.0 GenomicFeatures_1.10.2 >>> [15] GenomicRanges_1.10.7 genoset_1.10.1 >>> [17] Gviz_1.2.1 Hmisc_3.10-1 >>> [19] KernSmooth_2.23-9 labeling_0.1 >>> [21] lattice_0.20-13 lumi_2.10.0 >>> [23] MASS_7.3-23 Matrix_1.0-11 >>> [25] methylumi_2.4.0 mgcv_1.7-22 >>> [27] munsell_0.4 nleqslv_2.0 >>> [29] nlme_3.1-108 parallel_2.15.2 >>> [31] plyr_1.8 preprocessCore_1.20.0 >>> [33] RColorBrewer_1.0-5 RCurl_1.95-4.1 >>> [35] Rsamtools_1.10.2 rtracklayer_1.18.2 >>> [37] scales_0.2.3 splines_2.15.2 >>> [39] stats4_2.15.2 stringr_0.6.2 >>> [41] survival_2.37-4 tools_2.15.2 >>> [43] XML_3.95-0.2 xtable_1.7-1 >>> [45] zlibbioc_1.4.0 >>> >>> With regards, >>> >>> Lavinia Gordon >>> Senior Research Officer >>> Quantitative Sciences Core, Bioinformatics >>> >>> Murdoch Childrens Research Institute >>> The Royal Children's Hospital >>> Flemington Road Parkville Victoria 3052 Australia T 03 8341 6221 >>> www.mcri.edu.au<http: www.mcri.edu.au=""/> >>> >>> >>> ______________________________________________________________________ >>> This email has been scanned by the Symantec Email Security.cloud service. >>> For more information please visit http://www.symanteccloud.com >>> ______________________________________________________________________ >>> [[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 >> >> >> -- >> Computational Biology / Fred Hutchinson Cancer Research Center >> 1100 Fairview Ave. N. >> PO Box 19024 Seattle, WA 98109 >> >> Location: Arnold Building M1 B861 >> Phone: (206) 667-2793 >> >> ______________________________________________________________________ >> This email has been scanned by the Symantec Email Security.cloud service. >> For more information please visit http://www.symanteccloud.com >> >> If you have any question, please contact MCRI IT Helpdesk for further assistance. >> ______________________________________________________________________ >> >> ______________________________________________________________________ >> This email has been scanned by the Symantec Email Security.cloud service. >> For more information please visit http://www.symanteccloud.com >> >> _______________________________________________ >> 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 > > _______________________________________________ > 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