Just a vote for still allowing for multiple genomes in a Seqinfo object (in a GRanges object). My use case is in bisulfite-sequencing experiments where there is often a spike-in of a lambda phage genome along with the genome of interest (human or mouse). It's often useful to keep all data from a single library together in the same objet but process according to genome(x) for each seqlevel.
FWIW, I like Vincent's proposal of selectSome(unique(genome(x))) in the show method. Cheers, Pete > I might have requested the genome annotation, but I'm pretty sure it wasn't > me who decide on tracking it on a per-sequence basis. I could imagine use > cases for that though, e.g., when diagnosing sequencing contamination (like > human vs. mouse). But most other tools and file formats expect a single > genome per "track", so, for example, rtracklayer has an internal function > singleGenome() to take care of this. > > On Mon, Sep 8, 2014 at 10:50 AM, Herv? Pag?s <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 >> 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 >>> >>> >> -- >> 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...@fhcrc.org >> Phone: (206) 667-5791 >> Fax: (206) 667-1319 >> >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> -------------------------------- Peter Hickey, PhD Student/Research Assistant, Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Vic 3052, Australia. Ph: +613 9345 2324 hic...@wehi.edu.au http://www.wehi.edu.au ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:6}} _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
