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

[Peter Hickey]

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 <hpages at 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 at 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: hpages at fhcrc.org
>> Phone:  (206) 667-5791
>> Fax:    (206) 667-1319
>> 
>> 
>> _______________________________________________
>> Bioc-devel at 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

hickey at wehi.edu.au
http://www.wehi.edu.au

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