Instead of printing out multiple lines of a table that is rarely of interest, could we develop Peter's idea toward something like:
hg19:chr1 hg19:chr2 ... [lengths ...] Not sure what condensed notation would be useful for circularity. On Mon, Sep 8, 2014 at 5:21 PM, Peter Hickey <hic...@wehi.edu.au> wrote: > Perhaps it might be useful to have some way of highlighting if any of the > chromosomes are circular or highlighting if there are multiple genomes > present? Otherwise this information might be hidden in the "…" > > Cheers, > Pete > > > On 09/09/2014, at 9:44 AM, Hervé Pagès <hpa...@fhcrc.org> wrote: > > > On 09/08/2014 02:28 PM, Peter Hickey wrote: > >> 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. > > > > Note taken. Thanks Pete! It's always great to know about concrete use > > cases. > > > >> > >> FWIW, I like Vincent's proposal of selectSome(unique(genome(x))) in the > show method. > > > > Or what about displaying the genome next to the seqlevel it's > > associated with? Like e.g.: > > > > > gr > > GRanges with 3 ranges and 0 metadata columns: > > seqnames ranges strand > > <Rle> <IRanges> <Rle> > > [1] chr14 [19069583, 19069654] + > > [2] chr14 [19363738, 19363809] + > > [3] chr14 [19363755, 19363826] - > > [4] chr14 [19369799, 19369870] + > > --- > > seqinfo: > > seqlevels seqlengths isCircular genome > > chr1 249250621 <NA> hg19 > > chr10 135534747 <NA> hg19 > > chr11 135006516 <NA> hg19 > > ... ... ... ... > > chrUn_gl000249 38502 <NA> hg19 > > chrX 155270560 <NA> hg19 > > chrY 59373566 <NA> hg19 > > > > That way, we also raise awareness about the isCircular field. > > The current choice to only display the seqlengths pre-dates the > > existence of the seqinfo slot but might be a little bit misleading > > those days since it only exposes some arbitrary seqinfo fields. > > > > H. > > > >> > >> 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 > >> > > > > -- > > 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 > > -------------------------------- > 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 inte...{{dropped:12}} _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel