[Bioc-devel] Bioc-devel Digest, Vol 136, Issue 3

[Riccardo Romoli]

Hi, as Dan suggested after the update I get the same error as in Zin2... 
so I tried to isolate the error and it seems to be correlated wit the 
CAMERA package. Searching in the repos 
(http://bioconductor.org/checkResults/release/bioc-LATEST/CAMERA/zin2-checksrc.html) 
I found that the 'CAMERA guys' get the same error:

 > xsa <- annotate(xs) Start grouping after retention time. Created 14 
pseudospectra. Error in x$membership : $ operator not defined for this 
S4 class

What should I do now?

All the Best, Riccardo

On 03/07/15 12:00, bioc-devel-request at r-project.org wrote:
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> Today's Topics:
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>     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.COMMO at gustaveroussy.fr>
> To: Herv? Pag?s <hpages at fredhutch.org>,	"bioc-devel at r-project.org"
> 	<bioc-devel at r-project.org>
> Subject: Re: [Bioc-devel] SNPlocs.Hsapiens.dbSNP142.GRCh37
> Message-ID:
> 	<A7711FBBB22F044EB03FB64331E2B11A01B591E90F at 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 [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.
>
>
> 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
>>
> --
> 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: hpages at 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 <hpages at fredhutch.org>
> To: COMMO Frederic <Frederic.COMMO at gustaveroussy.fr>,
> 	"bioc-devel at r-project.org" <bioc-devel at r-project.org>
> Subject: Re: [Bioc-devel] SNPlocs.Hsapiens.dbSNP142.GRCh37
> Message-ID: <55956735.60402 at 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 [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.
>>
>>
>> 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
>>>
>> --
>> 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: hpages at fredhutch.org
>> Phone:  (206) 667-5791
>> Fax:    (206) 667-1319
>>

-- 
Riccardo Romoli, PhD
Mass Spectrometry Centre - CISM
University of Florence
Via Ugo Schiff 6, 50019 Sesto Fiorentino (FI), Italy
Phone: +39 055 4573783/2
email: riccardo.romoli at unifi.it
web site: www.cism.unifi.it