[BioC] methyAnalysis - changes to GenoSet
Lavinia Gordon
lavinia.gordon at mcri.edu.au
Mon Mar 11 22:13:51 CET 2013
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/>
>
>
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