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

[Hervé Pagès]

Salut Frédéric,

As I said, this is available in the new versions of BSgenome
(1.36.2 in release, 1.37.3 in devel) which will propagate
to the public repos in a couple of hours. So make sure to
run biocLite() (with no arguments) in a couple of hours to
get any update that will become available today. Then try again.

Cheers,
H.


On 07/02/2015 09:15 AM, COMMO Frederic wrote:
> Salut Hervé,
>
> 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 à demain..." :p
>
> Cheers,
> Fred
>
> Frederic Commo
> Bioinformatics, U981
> Gustave Roussy
>
> ________________________________________
> De : Hervé Pagès [hpages at fredhutch.org]
> Date d'envoi : mercredi 1 juillet 2015 20:25
> À : COMMO Frederic; bioc-devel at r-project.org
> Objet : Re: [Bioc-devel] SNPlocs.Hsapiens.dbSNP142.GRCh37
>
> 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]]
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages at fredhutch.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319