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

COMMO Frederic Frederic.COMMO at gustaveroussy.fr
Mon Jun 29 13:29:57 CEST 2015

Erratum: the rsiIds come from Affymetrix-SNP6.0, not cytoScanHD.

Frederic Commo
Bioinformatics, U981
Gustave Roussy

De : Bioc-devel [bioc-devel-bounces at r-project.org] de la part de COMMO Frederic [Frederic.COMMO at gustaveroussy.fr]
Date d'envoi : lundi 29 juin 2015 12:50
À : bioc-devel at r-project.org
Objet : [Bioc-devel] SNPlocs.Hsapiens.dbSNP142.GRCh37


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.
rsids <- c("rs10458597", "rs12565286", "rs7553394")
rsid2loc(rsids, caching=TRUE)


Frederic Commo
Bioinformatics, U981
Gustave Roussy

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