[Bioc-devel] should genome() be so complicated?/add genome report to GRanges show method
On Tue, Sep 9, 2014 at 12:30 AM, Herv? Pag?s <hpages at fhcrc.org> wrote:
On 09/08/2014 06:42 PM, Michael Lawrence wrote:
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.
I don't know either. I'm worried that this would make the seqinfo stuff look like a named vector and that the user would expect hg19:chr1, hg19:chr2, etc... to be valid names. With the table-like layout, some screen real estate can always be saved by printing less lines:
What I had in mind was
> gr
GRanges with 3 ranges and 0 metadata columns:
genome: hg19
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chr14 [19069583, 19069654] +
[2] chr14 [19363738, 19363809] +
[3] chr14 [19363755, 19363826] -
[4] chr14 [19369799, 19369870] +
you could then probably dispense with the seqlengths. i have never found them too useful except as a key to the genome. if there are multiple genomes, we have something like genomes: hg19, mm9 the point is to make it prominent, particularly at a time of transition.
--- seqinfo: 60 seqlevels (2 circulars) on 2 genomes (hg19, mm10) ---
seqlevels seqlengths isCircular genome
chr1 249250621 <NA> hg19
chr10 135534747 <NA> hg19
... ... ... ...
chrX 155270560 <NA> hg19
chrY 59373566 <NA> hg19
I agree that the exact content of the seqinfo table itself is rarely
of interest so printing only 3 or 4 lines is OK. IMO it's important
to make the user aware of the existence of this hidden table and to
display it like what it really is (i.e. a table). Also displaying the
column names is a well established tradition and serves the purpose
of providing a quick summary of the accessors that are available to
access those fields.
H.
On Mon, Sep 8, 2014 at 5:21 PM, Peter Hickey <hickey at wehi.edu.au
<mailto:hickey at 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, Herv? Pag?s <hpages at fhcrc.org
<mailto: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
<mailto: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 <mailto: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 <mailto:hpages at fhcrc.org>
>>>> Phone: (206) 667-5791 <tel:%28206%29%20667-5791>
>>>> Fax: (206) 667-1319 <tel:%28206%29%20667-1319>
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioc-devel at r-project.org <mailto:Bioc-devel at r-project.org>
mailing list
>>
>> --------------------------------
>> 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 <tel:%2B613%209345%202324>
>>
>> hickey at wehi.edu.au <mailto:hickey at wehi.edu.au>
>> http://www.wehi.edu.au
>>
>>
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>
> --
> 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 <mailto:hpages at fhcrc.org>
> Phone:(206) 667-5791 <tel:%28206%29%20667-5791>
> Fax:(206) 667-1319 <tel:%28206%29%20667-1319>
--------------------------------
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 <tel:%2B613%209345%202324>
hickey at wehi.edu.au <mailto:hickey at wehi.edu.au>
http://www.wehi.edu.au
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The information in this email is confidential and
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-- 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
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