OK so let's go for a 1 line summarization of the seqinfo.
Vince is that OK if we keep this at the bottom of the object?
That way it will always be visible, even when the object requires
more than 1 screen to display (e.g. when it has a lot of metadata
cols). Will look something like:
> 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: 60 seqlevels (2 circular) on 2 genomes (hg19, mm10); no
seqlengths
Thanks,
H.
On 09/09/2014 06:38 AM, Michael Lawrence wrote:
Agreed, that looks a lot nicer.
On Tue, Sep 9, 2014 at 4:42 AM, Martin Morgan <mtmor...@fhcrc.org> wrote:
On 09/09/2014 04:02 AM, Michael Lawrence wrote:
I'm in favor of this display. The seqinfo output at the bottom has always
been annoying (over-emphasized).
the fact that the lengths are 'NA' can be a helpful prompt to do something
about it, e.g., add seqinfo when inputting the data. Also they are helpful
when one is told that seqlengths are incompatible during, e.g.,
findOverlaps. But I like the idea of less but more informative display of
seqinfo, along the lines suggested by Vince.
seqinfo: 60 seqlevels (2 circular) on 2 genomes (hg19, mm10); 60 'NA'
seqlengths
Martin
On Mon, Sep 8, 2014 at 10:08 PM, Vincent Carey <
st...@channing.harvard.edu>
wrote:
On Tue, Sep 9, 2014 at 12:30 AM, Hervé Pagès <hpa...@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 <hic...@wehi.edu.au
<mailto: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
<mailto: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
<mailto: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 <mailto: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 <mailto:hpa...@fhcrc.org>
>>>> Phone: (206) 667-5791 <tel:%28206%29%20667-5791>
>>>> Fax: (206) 667-1319 <tel:%28206%29%20667-1319>
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioc-devel@r-project.org <mailto: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 <tel:%2B613%209345%202324>
>>
>> hic...@wehi.edu.au <mailto: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 <mailto: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 <mailto:hpa...@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>
hic...@wehi.edu.au <mailto:hic...@wehi.edu.au>
http://www.wehi.edu.au
____________________________________________________________
__________
The information in this email is confidential and
intend...{{dropped:8}}
_______________________________________________
Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org>
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list
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--
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
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--
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1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
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--
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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
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