[Bioc-devel] Bioc-devel Digest, Vol 136, Issue 3
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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https://stat.ethz.ch/mailman/listinfo/bioc-devel or, via email, send a message with subject or body 'help' to bioc-devel-request at r-project.org You can reach the person managing the list at bioc-devel-owner at r-project.org When replying, please edit your Subject line so it is more specific than "Re: Contents of Bioc-devel digest..." 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.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