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

Salut Herv?,

It sounds great, but according to the man page, snpsById() requires an 'XtraSNPlocs' object, and the only one availble on bioconductor is 'XtraSNPlocs.Hsapiens.dbSNP141.GRCh38'
I need to work with GRCh37 annotations.
Is there a trick to transform a 'SNPlocs' object, such as 'SNPlocs.Hsapiens.dbSNP142.GRCh37', into an 'XtraSNPlocs'?

"Ne remets jamais ? demain..." :p

Cheers,
Fred

Frederic Commo
Bioinformatics, U981
Gustave Roussy

________________________________________
De : Herv? Pag?s [hpages at fredhutch.org]
Date d'envoi : mercredi 1 juillet 2015 20:25
? : COMMO Frederic; bioc-devel at r-project.org
Objet : Re: [Bioc-devel] SNPlocs.Hsapiens.dbSNP142.GRCh37

Salut Fr?d?ric,

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.

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

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Herv? Pag?s

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