Erratum: the rsiIds come from Affymetrix-SNP6.0, not cytoScanHD.
Frederic Commo
Bioinformatics, U981
Gustave Roussy
________________________________________
De : Bioc-devel [bioc-devel-boun...@r-project.org] de la part de COMMO Frederic
[frederic.co...@gustaveroussy.fr]
Date d'envoi : lundi 29 juin 2015 12:50
À : bioc-devel@r-project.org
Objet : [Bioc-devel] SNPlocs.Hsapiens.dbSNP142.GRCh37
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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