[BioC] table for GenomicRanges

[Steve Lianoglou]

Hi,

On Wed, Dec 5, 2012 at 5:50 PM, Michael Lawrence
<lawrence.michael at 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