[Bioc-devel] SNPlocs.Hsapiens.dbSNP142.GRCh37

[Hervé Pagès]

Salut Frédéric,

I had this on my list for a long time so here it goes. Starting with
BSgenome 1.36.2 (in release) and 1.37.3 (in devel), a new API is
available for querying a SNPlocs object:

   snpsBySeqname()

   snpsByOverlaps()

   snpsById()

Note that this is the new recommended API. In particular snpsById() is
what should be used instead of rsid2loc(). It has an argument
(ifnotfound) that let's you control what to do if some SNP ids are
not found. See ?SNPlocs for more information and some examples.

These new versions of BSgenome should become available via biocLite()
in 24 hours or so. Let me know if you run into problems.

Cheers,
H.


On 06/29/2015 03:50 AM, COMMO Frederic wrote:
> Hi,
>
> I'm trying to map rsi Ids provided in the Affymetrix cytoScanHD arrays, using the 'SNPlocs.Hsapiens.dbSNP142.GRCh37' package, and rsid2loc().
>
> It turns out that some of these rsi ids are unknown, e.g. rsi7553394, and rsi2loc() fails on the entire search.
>
> It would be nice if rsi2loc() would catch the failures, then return the found and the unknown ids, separately, maybe as a list or in success/failure slots. So a multiple-Ids search would not fail.
>
> Maybe I missed something, and the function already handle errors.
>
> ## To reproduce
> ## "rs7553394" corresponds to probe SNP_A-1780654 in the Affy cytoScanHD, annotated in Hg19.
> library(SNPlocs.Hsapiens.dbSNP142.GRCh37)
> rsids <- c("rs10458597", "rs12565286", "rs7553394")
> rsid2loc(rsids, caching=TRUE)
>
> Fred
>
> Frederic Commo
> Bioinformatics, U981
> Gustave Roussy
>
> 	[[alternative HTML version deleted]]
>
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>

-- 
Hervé Pagès

Program in Computational Biology
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