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 comp
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
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
On Mon, Sep 8, 2014 at 1:50 PM, Hervé Pagès 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
>
i would propose that it show selectSome(unique(genome(x))) -- seems
consistent with the multi
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
g
On 09/08/2014 11:41 AM, Michael Lawrence wrote:
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.
OK, maybe. Don't trust my memory too much on this. No regrets though.
I think it was the right thing to do ;-) Just b
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 mou
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 wrote:
> On 09/08/2014 02:28 PM,
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.
On Mon, Sep 8, 2014 at 5:21 PM, Peter Hickey wrote:
> Per
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 k
On Tue, Sep 9, 2014 at 12:30 AM, Hervé Pagès 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 ...]
>>
>> No
I'm in favor of this display. The seqinfo output at the bottom has always
been annoying (over-emphasized).
On Mon, Sep 8, 2014 at 10:08 PM, Vincent Carey
wrote:
>
>
> On Tue, Sep 9, 2014 at 12:30 AM, Hervé Pagès wrote:
>
>> On 09/08/2014 06:42 PM, Michael Lawrence wrote:
>>
>>> Instead of print
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 a
Agreed, that looks a lot nicer.
On Tue, Sep 9, 2014 at 4:42 AM, Martin Morgan 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
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
GRa
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