[Bioc-devel] should genome() be so complicated?/add genome report to GRanges show method

[Hervé Pagès]

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 at 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: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319