[BioC] methyAnalysis - changes to GenoSet

Tim Triche, Jr. tim.triche at gmail.com
Tue Mar 12 16:32:19 CET 2013 

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 âGenoSet#character#ANY#ANYâ chosen for
>>> function â[â, target signature âMethyGenoSet#character#character#missingâ.
>>> "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

More information about the Bioconductor mailing list