[BioC] c()ombining G/IRanges with elementMetadata: feature inquiry/request

[Steve Lianoglou]

On Mon, Feb 7, 2011 at 1:08 PM, Michael Lawrence
<lawrence.michael at gene.com> wrote:
>
> On Mon, Feb 7, 2011 at 9:42 AM, Steve Lianoglou
> <mailinglist.honeypot at gmail.com> wrote:
>>
>> Hi all,
>>
>> Would anyone else find it useful to have something like an
>> ".ignoreValues" argument in the `c`ombine functions for G/IRanges so
>> that you could easily combine several *Ranges objects that have
>> different elementMetadata.
>>
>> For instance:
>>
>> R> library(GenomicRanges)
>> R> gr.1 <- GRanges('chr1', IRanges(c(1, 10, 30), width=5), '*',
>> score=rnorm(3))
>> R> gr.2 <- GRanges('chr2', IRanges(c(20, 50, 100), width=10), '*',
>> annotation=c('a', 'b', 'c'))
>>
>> Now say I want to combine them:
>>
>> R> c(gr.1, gr.2)
>> Error in .Method(..., deparse.level = deparse.level) :
>>  column names for arg 2 do not match those of first arg
>>
>> It makes sense to error on that, since I'm losing information by
>> combining the two, but suppose that I know I'm going to lose
>> information but want to combine them anyway, I have to:
>>
>> R> values(gr.1) <- NULL
>> R> values(gr.2) <- NULL
>> R> c(gr.1, gr.2)
>>
>> Which would work, but if I didn't want to lose my elementMetadata, I'd
>>  make temp vars for gr.1 and gr.2 and set their values() to NULL then
>> combine the two (three, four, etc.)
>>
>> But what if something like this was kosher:
>>
>> R> c(gr.1, gr.2, .ignoreValues=TRUE)
>>
>
> Pretty good idea. Might name that parameter .ignoreElementMetadata. Longer,
> yes, but ignoreValues just sounds too generic.

I'm fine with either one, but I thought that the `values()`
function/idiom was introduced after `elementMetadata` came into play
simply because `elementMetadata` was a bit too cumbersome for
something that people used often.

I'm curious what the folks at The Hutch had in mind with respect to
how they envisioned the `elementMetadata` vs. `values` api to play
out?

> Also realize that these
> objects have a "metadata" slot in addition to elementMetadata. Not sure how
> that is currently combined/handled.

Good point. It looks like the metadata from the first I/GRanges object
is the only one that's kept, and the rest of the metadata is dropped
after they are combined. Perhaps something to think about more(?).

> Another addition could be a function that drops the metadata, just how
> unname drops the names of something.
>
> Then: c(dropMetadata(gr.1), dropMetadata(gr.2))

I guess it would have to be dropElementMetadata(..) since, `metadata`
and `elementMetadata` are two different beasts. Alternatively, we can
have an `unvalue(gr.1)`, which is somehow close to "unname"  :-)

> But yea, your idea for 'c' is convenient. Care to submit a patch?

I'd be happy to ... maybe just as soon as we get a green light from
The Hutch (w.r.t utility and param. name)?

Thanks,
-steve

>
> Thanks,
> Michael
>
>> and returned the combination of the "range" information of the desired
>> objects, with a NULL DataFrame for its elementMetadata?
>>
>> Looking at the source for the I/GRanges "c" functions, it looks like a
>> pretty easy change to make, but perhaps it's not worth adding an extra
>> parameter if others wouldn't find it useful.
>>
>> ... just ruminating some ...
>>
>> Thanks,
>>
>> -steve
>> --
>> 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
>>
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>
>



-- 
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