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> 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"
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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
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E-mail: hpa...@fhcrc.org
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Fax: (206) 667-1319
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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
hic...@wehi.edu.au
http://www.wehi.edu.au
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