Thanks, I've changed it to biocViews: Software, DataImport, DataRepresentation, Preprocessing
Cheers, Marcin 2015-12-02 22:52 GMT+01:00 Hervé Pagès <hpa...@fredhutch.org>: > Hi Marcin, > > BTW I noticed that RTCGA has no biocViews (only Software). Populating > the biocViews field with appropriate and specific terms will make > your packages show up in the corresponding views here > > http://bioconductor.org/packages/release/BiocViews.html#___Software > > and thus will greatly improve the chances that the user in the need > of functionalities like the ones you provide will discover your package. > > Cheers, > H. > > > On 11/22/2015 10:39 AM, Morgan, Martin wrote: > >> Marcin -- I join with Herve in strongly discouraging you from this >> approach. Because you wish only to change upper versus lower case of your >> package name, and because some operating systems ignore case, your package >> will go through a release where it is not available under either upper- or >> lower-case variant. This will confuse and alienate your users, even more >> than changing the package name to something completely different. There are >> a number of packages, including some of our own, where the name could have >> been chosen more carefully, but we have learned to live with our changes of >> mind. After all, you can still claim to be consistent with the naming >> convention of the RTCGA.clinical and RTCGA.mutations package ;) >> >> I guess Dario was referring to >> >> library(AnnotationHub) >> hub = AnnotationHub() >> eset = query(hub, "GSE62944")[[1]] >> >> with >> >> eset >>> >> ExpressionSet (storageMode: lockedEnvironment) >> assayData: 23368 features, 7706 samples >> element names: exprs >> protocolData: none >> phenoData >> sampleNames: TCGA-02-0047-01A-01R-1849-01 >> TCGA-02-0055-01A-01R-1849-01 ... TCGA-ZG-A8QZ-01A-11R-A37L-07 (7706 >> total) >> varLabels: bcr_patient_barcode bcr_patient_uuid ... CancerType (421 >> total) >> varMetadata: labelDescription >> featureData: none >> experimentData: use 'experimentData(object)' >> Annotation: >> >>> table(eset$CancerType) >>> >> >> BLCA BRCA COAD GBM HNSC KICH KIRC KIRP LAML LGG LIHC LUAD LUSC OV >> PRAD READ >> 273 1082 468 170 481 66 540 226 164 528 212 514 490 344 >> 423 164 >> SKCM STAD THCA UCEC >> 373 146 506 536 >> >>> print(object.size(eset), units="auto") >>> >> 264.5 Mb >> >>> ov = eset[, eset$CancerType == "OV"] ## ovarian samples >>> >> >> The data are Rsubread summarized counts from before the May update. In >> the near term, we are actively expanding offerings derived from that GSE to >> include the May update; this is in conjunction with efforts to develop an >> 'ExperimentHub' analog of AnnotationHub, for more experiment-centric, >> heavily curated resources. >> >> It is a little unclear whether the AnnotationHub and your data are >> redundant or complementary, and whether they can be combined into a single >> offering. One philosophical difference is the use of semantically rich and >> integrated ExpressionSet versus basic data structures (data.frame, in your >> case). We also differ in when we separate data into cancer types; we opted >> for the entire data set because it is not impossibly large. And our data >> are AnnotationHub-based rather than package-based. Obviously, avoiding >> redundant access to the same data is beneficial. One possibility is to >> collaboratively curate the data into AnnotationHub / ExperimentHub >> resources, and to tailor access via packages that reference the resource >> (e.g., one can retrieve the GRASP2 data base through AnnotationHub as >> resource AH21414, or via grasp2db::GRASP2(); the latter comes with >> documentation for manipulating the resource). >> >> It seems like there are similar opportunities for collaboration and >> reduced redundancy between the RTCGA, RTCGAToolbox, and TCGAbiolinks >> packages. >> >> Martin Morgan >> Bioconductor >> >> ________________________________________ >> From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Marcin >> Kosiński [m.p.kosin...@gmail.com] >> Sent: Sunday, November 22, 2015 11:37 AM >> To: Dario Strbenac >> Cc: bioc-devel@r-project.org >> Subject: Re: [Bioc-devel] Is there a way to change the name of R package >> that is already published on bioconductor? >> >> Hi Herve, >> >> I think I would like to proceed with such technical possibility. >> I'd like to keep consistency with the RTCGA.miRNASeq package that I am >> uploading to bioconductor with issue 1335. >> Can we schedule such operation? >> >> Best, >> Marcin >> >> >> >> Hi Dario, >> >> Do you want to tell me that there is a possibility to load RNASeq datasets >> for all available 38 cancer types/cohorts from the last release date >> (21-08-2015) of datasets from The Cancer Genome Atlas with the use of >> AnnotationHub? >> >> Is it as simple as: >> >> library(AnnotationHub) >> BRCA.RNASeq -> x >> >> ? >> >> Best, >> Marcin >> >> 2015-11-17 0:00 GMT+01:00 Dario Strbenac <dstr7...@uni.sydney.edu.au>: >> >> Hello, >>> >>> How does your package differ to importing GSE62944 into R with >>> AnnotationHub >>> http://bioinformatics.oxfordjournals.org/content/31/22/3666.long ? It >>> seems like unnecessary duplication. >>> >>> -------------------------------------- >>> Dario Strbenac >>> PhD Student >>> University of Sydney >>> Camperdown NSW 2050 >>> Australia >>> _______________________________________________ >>> Bioc-devel@r-project.org mailing list >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>> >>> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> >> >> This email message may contain legally privileged and/or confidential >> information. If you are not the intended recipient(s), or the employee or >> agent responsible for the delivery of this message to the intended >> recipient(s), you are hereby notified that any disclosure, copying, >> distribution, or use of this email message is prohibited. If you have >> received this message in error, please notify the sender immediately by >> e-mail and delete this email message from your computer. Thank you. >> _______________________________________________ >> Bioc-devel@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: hpa...@fredhutch.org > Phone: (206) 667-5791 > Fax: (206) 667-1319 > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel