On Mon, Sep 8, 2014 at 1:50 PM, Hervé Pagès <hpa...@fhcrc.org> wrote:
> Hi Vince, > > Yes it would make sense to have the "show" method report the genome > when genome(x) contains a unique non-NA value. I think the main > i would propose that it show selectSome(unique(genome(x))) -- seems consistent with the multiple genomes in use when relevant if NA, IHMO that is an important lack of metadata and people should see that then as well > use case for having the genome defined at the sequence level instead > of the whole object level is metagenomics. Maybe Michael has some other > good use cases to share since IIRC he requested the addition of the > genome field a couple of years ago and made the case for having it > defined at the sequence level. > > Cheers, > H. > > > On 09/08/2014 07:21 AM, Vincent Carey wrote: > >> For GRanges x, my naive expectation is that genome(x) returns a length- >> >> one tag identifying the genome to which chromosomal coordinates >> >> correspond. The genome() method seems to have sequence-specific >> >> semantics, which makes sense, but when we identify sequence >> >> with chromosome, it seems too complicated. Is there a use case for >> >> a GRanges with sequences from several different genomes? >> >> >> One reason I am inquiring is that I feel it would be nice to have the >> GRanges show() method report, prominently, the genome in use (or NA >> >> if unspecified). This could be accomplished by reporting >> unique(genome(x)), and perhaps that would be satisfactory. >> >> after example(genome) : >> >> seqinfo(txdb) >>> >> >> Seqinfo of length 15 >> >> seqnames seqlengths isCircular genome >> >> CH2L 23011544 FALSE dm3 >> >> CH2R 21146708 FALSE dm3 >> >> CH3L 24543557 FALSE dm3 >> >> CH3R 27905053 FALSE dm3 >> >> CH4 1351857 FALSE dm3 >> >> ... ... ... ... >> >> CH3LHet 2555491 FALSE dm3 >> >> CH3RHet 2517507 FALSE dm3 >> >> CHXHet 204112 FALSE dm3 >> >> CHYHet 347038 FALSE dm3 >> >> CHUextra 29004656 FALSE dm3 >> >> genome(seqinfo(txdb)) >>> >> >> CH2L CH2R CH3L CH3R CH4 CHX CHU M >> >> "dm3" "dm3" "dm3" "dm3" "dm3" "dm3" "dm3" "dm3" >> >> CH2LHet CH2RHet CH3LHet CH3RHet CHXHet CHYHet CHUextra >> >> "dm3" "dm3" "dm3" "dm3" "dm3" "dm3" "dm3" >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> 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...@fhcrc.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
