The manifest has probe locations, but they're keyed against which build
they were designed to.  So for example, about half the CpH probes are built
against hg18/GRCh36 instead of hg19/GRCh37.  I put together a probe package
that attempts to make some sense of what is meant by 'strand' for
Illumina's probes, the corresponding genomic forward sequence, and where
the CpG goes.

 When using that approach, the interrogated CpG or CpH locus always appears
at 'site' and extends 1 (for CpG) or 2 (for CpH) probes upstream of the
site.  So if I want to look for CpGs that overlap a SNP, using SNPlocs and
GenomicRanges, it is enough to subsetOverlaps() and tabulate them.   Same
for HapMap SNPs, or H3K4Me2 enriched sites in a particular tissue type,
DNAse hypersensitive sites, or what have you.  The GRanges approach is just
far more flexible than the gene-centric approach.

So, I added a couple of "freeze-dried" GRanges objects to
IlluminaHumanMethylation450k.db version 2.0+ , which are returned by
getCpGR() and getCpHR(), to return GRanges objects with these data
included.  The probe package mostly just adds sequences into the mix, so
that all of this can be verified against one's genomic build of choice.


On Mon, Nov 7, 2011 at 3:00 PM, Dario Strbenac <D.Strbenac@garvan.org.au>wrote:

> Thanks for the explanations. Do you know of a persistent source of
> mappings of probes to genomic locations, such as :
>
> |-----------------------------------
> |probe_id  | chr   | pos |  strand |
> |-----------------------------------
>
> This might be useful if, for example, I wanted to write a BED file out to
> use with a genome browser. I suppose it's possible to map the probes
> ourselves, but I was thinking of it being more reproducible and citable if
> some Bioconductor package had already published this.
>



-- 
If people do not believe that mathematics is simple,
it is only because they do not realize how complicated life is. John von
Neumann<http://www-groups.dcs.st-and.ac.uk/~history/Biographies/Von_Neumann.html>

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