that's cool, then it's consistent with score() and friends... this sounds
like a grand scheme



On Wed, Dec 5, 2012 at 4:31 PM, Hervé Pagès <hpages@fhcrc.org> wrote:

> So with tally, what would be the name of the metadata col? Would "tally"
> be OK?
>
> It's kind of neat to use the same name for the metadata col as for the
> function itself. That makes the code more readable:
>
>   mcols(count(gr))$count
>
> Thanks for the feedback,
> H.
>
>
>
> On 12/05/2012 03:05 PM, Tim Triche, Jr. wrote:
>
>> that goes along nicely with BamTally in gmapR, which is a damn useful
>> function IMHO... actually I think I wrote a tally() function or
>> something like it for Rsubread, can't remember whether I sent it in with
>> the patch though.  Anyways, a running tally is a good mental image for
>> this functionality
>>
>>
>>
>>
>> On Wed, Dec 5, 2012 at 2:59 PM, Steve Lianoglou
>> <mailinglist.honeypot@gmail.**com <mailinglist.honeypot@gmail.com><mailto:
>> mailinglist.honeypot@**gmail.com <mailinglist.honeypot@gmail.com>>>
>>
>> wrote:
>>
>>     Hi,
>>
>>     On Wed, Dec 5, 2012 at 5:50 PM, Michael Lawrence
>>     <lawrence.michael@gene.com <mailto:lawrence.michael@gene.**com<lawrence.michael@gene.com>>>
>> wrote:
>>      > The question is whether there is ever a use case to have a simple
>>     table.
>>      > This is analogous to base R's table and data.frame. For example,
>>     if you
>>      > call xtabs(), you get a table, then you have to call
>>     as.data.frame to get
>>      > back into the data.frame context. This is sort of clean, and we
>> could
>>      > create an extension of table that for efficiency stores the
>>     associated
>>      > GRanges along with the counts in the .Data slot. Then as(x,
>>     "GRanges") on
>>      > that would generate the GRanges with the count column. That would
>> be
>>      > complicated though.
>>      >
>>      > Another issue is that table() cannot be used in the general way,
>>     due to
>>      > restrictions on dispatch with "...".
>>      >
>>      > So I think I'm in favor of a new "count" generic. That naming is
>>     consistent
>>      > with countOverlaps, countSubjects, countQueries, etc.
>>
>>     Or maybe `tally`? Somehow I have a mental association w/ that being
>>     closer to `tabulate`, but I guess it's really not and maybe it's just
>>     me that has a mind map that puts `tally` closer to `table` than
>>     `count` is .
>>
>>     --
>>     Steve Lianoglou
>>     Graduate Student: Computational Systems Biology
>>       | Memorial Sloan-Kettering Cancer Center
>>       | Weill Medical College of Cornell University
>>     Contact Info: http://cbio.mskcc.org/~lianos/**contact<http://cbio.mskcc.org/~lianos/contact>
>>
>>
>>
>>
>> --
>> /A model is a lie that helps you see the truth./
>> /
>> /
>> Howard Skipper
>> <http://cancerres.**aacrjournals.org/content/31/9/**1173.full.pdf<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>
>> >
>>
>>
> --
> 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: hpages@fhcrc.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>



-- 
*A model is a lie that helps you see the truth.*
*
*
Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>

	[[alternative HTML version deleted]]

