[Bioc-devel] should genome() be so complicated?/add genome report to GRanges show method
Peter Hickey
hickey at wehi.EDU.AU
Tue Sep 9 02:21:23 CEST 2014
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 <hpages at 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 <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
>>
>> ______________________________________________________________________
>> The information in this email is confidential and intend...{{dropped:6}}
>>
>> _______________________________________________
>> 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
--------------------------------
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
______________________________________________________________________
The information in this email is confidential and intend...{{dropped:8}}
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