[BioC] minfi - how to subset a GenomicMethylSet by chromosome/seqname

[Toby Hughes]

Thanks Martin.  Will try this one as well.

Kind regards,

Toby.

-----Original Message-----
From: Martin Morgan [mailto:mtmorgan at fhcrc.org] 
Sent: Friday, 11 January 2013 5:02 AM
To: ttriche at usc.edu
Cc: Tim Triche, Jr.; Toby Hughes; bioconductor at r-project.org
Subject: Re: [BioC] minfi - how to subset a GenomicMethylSet by chromosome/seqname

On 01/10/2013 10:15 AM, Tim Triche, Jr. wrote:
> I do this all the time with SEs, so here's a couple of options.
>
> ## keepSeqlevels generic
> setMethod("keepSeqlevels", signature(x="SummarizedExperiment", value="ANY"),
>            function(x, value) { # {{{
>              y <- which(rownames(x) %in%
> names(keepSeqlevels(rowData(x),value)))
>              return(x[y, ])
>            }) # }}}
> gmset.noXY <- keepSeqlevels(gmset, paste0('chr', 1:22))

?seqlevels<- has comparable behavior (in-place restriction to a subset of levels); after example(SummarizedExperiment)

 > seqlevels(sset)
[1] "chr1" "chr2"
 > seqlevels(sset, force = TRUE) <- "chr2"
 > seqlevels(sset)
[1] "chr2"


>
> ## or use split; this is slower and balkier than keepSeqlevels 
> gmset.noXY <- split(gmset, as.vector(seqnames(gmset)))[ paste0('chr', 
> 1:22) ]
>
> ## bonus: masking, cf. MM
> load("maskedRegions.rda")
> gmset <- gmset[ countOverlaps(gmset, maskedRegions) == 0, ]
>
> ## or perhaps gmset[ !gmset %within% maskedRegions, ] ... ?
>
> there is a small pile of functions like this (combine(), combine(, 
> withNAs=TRUE), keepSeqlevels(), etc.) I'd like to see as generics for 
> all SummarizedExperiments in GenomicRanges.  Let the appropriate 
> people know if you agree with this notion and any pitfalls you foresee
>
>
> --t
>
>
>
>
>
> On Thu, Jan 10, 2013 at 5:01 AM, Toby Hughes <toby.hughes at adelaide.edu.au>wrote:
>
>> Hi all,
>>
>> I am relatively new to both R and the Bioconductor packages, so 
>> apologies if this is a naïve question.  I am using minfi to 
>> preprocess a small set
>> (60 samples) of Illumina450k microarray data.  I have got to the 
>> point where I have a GenomicMethylSet, following the use of 
>> mapToGenome on a MethylSet to provide annotation, having excluded 
>> those probes without a defined position in the process.  I now wish 
>> to exclude probes from the sex chromosomes before using dmpFinder, 
>> and so I am seeking to subset the GenomicMethylSet to the autosomes 
>> only.  Despite days of searching and a number of references saying 
>> this is relatively straightforward, I have not yet had any success 
>> (have been exploring GenomicRanges).  Could someone please point me in the right direction with a code snippet or a reference?
>>
>> Kind regards,
>>
>> Toby.
>>
>>          [[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
>>
>>
>
>
>
>
> _______________________________________________
> 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