[BioC] IlluminaHumanMethylation450k.db: Missing probes in IlluminaHumanMethylation450kPROBELOCATION function?

[Simone]

Dear Tim,

> You will need to use toggleProbes() to get all probe locations (this is an
> undesirable side effect of the db0 package infrastructure, which is geared
> towards expression arrays where probes that map to multiple accessions are a
> "bad thing", and that is the reason I deprecated the 27k.db and 450k.db
> packages).

I understand. However, also with toggleProbes() I have got a problem.
I tried for example:

> x <- toggleProbes(IlluminaHumanMethylation450kPATH2PROBE, "all")

Error in (function (classes, fdef, mtable)  :
  unable to find an inherited method for function ‘toggleProbes’ for
signature ‘"AnnDbBimap"’

But for example the following works

> x <- toggleProbes(IlluminaHumanMethylation450kENSEMBL2PROBE, "all")

However, I would need the location information, so the column
"transcript_location" (e.g. 5'UTR, TSS200, Body, etc.) and it seems
that I cannot get it like this?

> The FDb.InfiniumMethylation packages have the locations of the targeted CpGs
> (and CpHs, and SNPs) for the corresponding build (just for the record, the
> genome build targeted by 450k.db is hg19/GRch37), but they are returned
> using get450k() or get27k() as a GRanges object.

Currently, this doesn't work for me neither (see my previous post).
Probably I'm doing something wrong ...

> Essentially, the mistake I made in compiling the 27k.db and 450k.db packages
> was to use an expression-centric (or gene- and transcript-centric)
> infrastructure to represent probes targeting individual loci.  It's more
> useful to think of the 450k array, in particular, as a SNP array, with
> functions for a given target locus inferred after discovery.  It's also more
> useful to think of the chip as a SNP array when considering differentially
> methylated regions, which could be loosely regarded as the methylation
> equivalent of copy number variations.  Last but not least, you can in fact
> use the array to estimate copy number along the genome, as for determining
> sex from chrX copy number.

Thank you for your hints and explanations!
But at the moment I am still stucked at a much simpler step, I would
just need an easy way to distinguish probes located in promoters from
those located in gene bodies (and to discard those which are annotated
to both).

Best wishes,
Simone