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Today's Topics:
1. Re: SNPlocs.Hsapiens.dbSNP142.GRCh37 (COMMO Frederic)
2. Re: SNPlocs.Hsapiens.dbSNP142.GRCh37 (Herv? Pag?s)
3. Re: Flagme creating vignettes ERROR (Dan Tenenbaum)
----------------------------------------------------------------------
Message: 1
Date: Thu, 2 Jul 2015 16:15:39 +0000
From: COMMO Frederic <frederic.co...@gustaveroussy.fr>
To: Herv? Pag?s <hpa...@fredhutch.org>, "bioc-devel@r-project.org"
<bioc-devel@r-project.org>
Subject: Re: [Bioc-devel] SNPlocs.Hsapiens.dbSNP142.GRCh37
Message-ID:
<a7711fbbb22f044eb03fb64331e2b11a01b591e...@srv-mbx-02.intra.igr.fr>
Content-Type: text/plain; charset="iso-8859-1"
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 [hpa...@fredhutch.org]
Date d'envoi : mercredi 1 juillet 2015 20:25
? : COMMO Frederic; bioc-devel@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.
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@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Herv? Pag?s
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: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319
------------------------------
Message: 2
Date: Thu, 02 Jul 2015 09:30:45 -0700
From: Herv? Pag?s <hpa...@fredhutch.org>
To: COMMO Frederic <frederic.co...@gustaveroussy.fr>,
"bioc-devel@r-project.org" <bioc-devel@r-project.org>
Subject: Re: [Bioc-devel] SNPlocs.Hsapiens.dbSNP142.GRCh37
Message-ID: <55956735.60...@fredhutch.org>
Content-Type: text/plain; charset=windows-1252; format=flowed
Salut Fr?d?ric,
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 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 [hpa...@fredhutch.org]
Date d'envoi : mercredi 1 juillet 2015 20:25
? : COMMO Frederic; bioc-devel@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.
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@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Herv? Pag?s
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: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319
