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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Program in Computational Biology
Division of Public Health Sciences
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