It's in there, simply not exported (d'oh!!!).  IF need be you can use

IlluminaHumanMethylation450k.db:::IlluminaHumanMethylation450kSNP
IlluminaHumanMethylation450k.db:::IlluminaHumanMethylation450kSNP10
IlluminaHumanMethylation450k.db:::IlluminaHumanMethylation450kSTRAND

to do these things.  (I recognize that I am somewhat of a bad person for
suggesting it, but it's the least of my sins)

Note the handy abbreviations for minimal typing.


On Mon, Aug 1, 2011 at 12:19 PM, Wong, Chao-Jen <cwon2@fhcrc.org> wrote:

> Hi, Khadeeja,
>
> Accession number and regulatory group can be found in
> IlluminaHumanMethylation450k.db.  Unfortunately this database package does
> not have snp10. The easiest way I found is exporting those information
> (snp10 and UCSC refname) along with the probe intensity data from
> GenomeStudio. If anyone has better solution, please let me know.
>
> As for for snp probes, you can easily tell from the probe IDs as snp probe
> ID always start with rsxxxx.
>
>
> Cheers,
> Chao-Jen
>
> ----- Original Message -----
> From: "khadeeja ismail" <hajjja@yahoo.com>
> To: bioconductor@r-project.org
> Sent: Monday, August 1, 2011 1:25:54 AM
> Subject: Re: [BioC] Probe ID to Sequence
>
> Hi,
>
> I need to find the following information for my
> IlluminaHumanMethylation450k probes but have no clue which packages I need.
>
> --Probe SNPs, SNP10
> --UCSC refgene name, group and accession number.
>
> I've come across SNPlocs.Hsapiens.dbSNP.20101109, GenomicRanges,
> GenomicFeatures as any related packages, but cannot see how I can use these.
>
> Any help is most appreciated.
>
> Best Regards,
> Hajja
>
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>
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>
> --
> Chao-Jen Wong
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Avenue N., M1-B514
> PO Box 19024
> Seattle, WA 98109
> 206.667.4485
> cwon2@fhcrc.org
>
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>



-- 
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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