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

[Simone]

Dear James,

> You would be better off using the FDb.InfiniumMethylation.hg19 package,
> which not only has all the locations for the probes, but also has them in a
> more useful format.
>
>> library(FDb.InfiniumMethylation.hg19)
>> x <- get450k()

Thanks for the suggestion. For some reason this does not work here. I
get the following error:

Error in `seqinfo<-`(`*tmp*`, value = NULL) :
  the supplied 'seqinfo' must be a Seqinfo object
In addition: Warning message:
In if (is.na(genome(GR))) { :
  the condition has length > 1 and only the first element will be used

> GRanges with 485577 ranges and 7 metadata columns:
>              seqnames               ranges strand   | addressA addressB
> channel
> <Rle> <IRanges> <Rle>   | <Rle> <Rle> <Rle>
>   cg13869341     chr1       [15865, 15866]      *   | 62703328 16661461
> Red
>   cg14008030     chr1       [18827, 18828]      *   | 27651330 <NA>    Both
>   cg12045430     chr1       [29407, 29408]      *   | 25703424 34666387
> Red
>   cg20826792     chr1       [29425, 29426]      *   | 61731400 14693326
> Red
>   cg00381604     chr1       [29435, 29436]      *   | 26752380 50693408
> Red

Would there also be a possibility to get directly the information
where in the gene the probes are located? For example, when I use
IlluminaHumanMethylation450kPROBELOCATION I get information like this:

    probe_id transcript_location
1 cg00035864   NR_001550:TSS1500
2 cg00050873   NM_001164471:Body
3 cg00050873   NR_001553:TSS1500
4 cg00061679      NM_004081:Body
5 cg00061679      NM_020420:Body
6 cg00061679   NM_001005375:Body

>From this I can easily extract the corresponding annotations (1stExon,
3'UTR, 5'UTR, Body, TSS1500, TSS200). In your sample above I do not
see anything like this, but I read something about annotateGRanges and
annotateDMRInfo, probably they would help, but because of the problem
above I still could not try. In the vignette you mentioned I couldn't
find an example retrieving this information at first sight, but I'll
have a closer look on it.

Best wishes,
Simone