[BioC] interpretation & visualization methylation data (illum 450k)

Fri Oct 12 04:59:30 CEST 2012

Just in case you have not seen this (because I think I forgot to
describe it in the manual), we now have
  mapToGenome
which easily adds genomic coordinates to your MethylSet.  From then on
you will be on your own, although we do expect to provide
functionality for annotation results "soon" (when we have completed
our current task of adding our DMR finder).

Kasper

On Thu, Oct 11, 2012 at 5:38 PM, Hooiveld, Guido <Guido.Hooiveld at wur.nl> wrote:
> Hi,
> We are analyzing our first methylation dataset (Illumina 450k array).
> Through minfi I am able obtain a list of differential methylated probes (CGxxxx), but I would like to place these in a genomic context. Unfortunately I don't have any hands-on experiences with genome analysis (genomic localization, closest transcript/gene, generating input for genome browser, etc.) so I would appreciate if someone could point my to a workflow that allows these type of analysis starting from a list of probes. I know packages such as GenomicRanges and GenomicFeatures likely can be used for this, but whether these are really the best options, and if so, the exact order/way isn't clear to me yet. Hence, any suggestion is appreciated.
>
> Thanks in advance,
> Guido
> ---------------------------------------------------------
> Guido Hooiveld, PhD
> Nutrition, Metabolism & Genomics Group
> Division of Human Nutrition
> Wageningen University
> Biotechnion, Bomenweg 2
> NL-6703 HD Wageningen
> the Netherlands
> tel: (+)31 317 485788
> fax: (+)31 317 483342
> email:      guido.hooiveld at wur.nl
> internet:   http://nutrigene.4t.com
> http://scholar.google.com/citations?user=qFHaMnoAAAAJ
> http://www.researcherid.com/rid/F-4912-2010
>
>
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