On Mon, Feb 20, 2012 at 4:33 PM, Martin Morgan <mtmorgan@fhcrc.org> wrote:

> On 02/20/2012 11:50 AM, Tengfei Yin wrote:
>
>> +1 for Tim's methods.....especially the $ and $<- method, it's always in a
>> wishlist for me :)
>>
>> well, maybe "$ " could be sometimes confusing when people trying to treat
>> GRanges as a general format similar to data.frame, and do something like
>> gr$seqnames<- blabla, the good part about current API is that it remind me
>> the difference bettween  elementMetadata and three required fields... but
>>
>
> GRanges extends Vector and
>
> > gr = GRanges("A", IRanges(1:10, 20), X=1:10, Y=1:10)
> > length(gr)
> [1] 10
> > length(values(gr))
> [1] 2
>
> shows the geometry -- one would expect gr$foo to access the range named
> 'foo' rather than the column of elementMetadata named 'foo'. I think this
> is the crux of the resistance.
>
>
Right, thanks for reiterating this. The question is whether the convenience
of the shortcut outweighs the conceptual inconsistency. Probably depends
heavily on one's perspective. I would favor the perspective of the frequent
user.


> When Tim says
>
>
> On 02/20/2012 11:45 AM, Tim Triche, Jr. wrote:
> > if these don't belong in BiocGenerics, I don't know what does :-D
>
> I'm not sure if the reference is to "intersect" (which is already in
> BiocGenerics), "%i%" etc., or to $ and $<-. For $ and $<-, they don't need
> to be in BiocGenerics because they are already made generics by the methods
> package -- BiocGenerics is meant to provide a place to define generics that
> would otherwise be defined independently in multiple packages.
>
> Martin
>
>
>  it will be convenient if general $ method support replacement? even for
>> seqnames, strand and ranges part? with default checking?
>>
>> other methods mentioned by Tim are also handy if default of those function
>> is under assumption.
>>
>> On Mon, Feb 20, 2012 at 1:04 PM, Michael Lawrence<lawrence.michael@**
>> gene.com <lawrence.michael@gene.com>
>>
>>> wrote:
>>>
>>
>>  On Mon, Feb 20, 2012 at 10:36 AM, Steve Lianoglou<
>>> mailinglist.honeypot@gmail.com**>  wrote:
>>>
>>>  Hi Tim,
>>>>
>>>> These functions are quite handy ... definitely going to poach them.
>>>>
>>>>
>>>
>>> I wonder if we should keep poaching these in the wild or if Bioc Core
>>> will
>>> ever bow to popular pressure and allow their inclusion in the base
>>> packages? ;-)
>>>
>>>
>>>  Also ... you need an editor with better code folding support ;-)
>>>>
>>>> Pual,
>>>>
>>>> Aslo, to do what you want to do, namely:
>>>>
>>>>
>>>>>
>>>>  extra.blank<-matrix(data=NA,**nrow=length(a.grs),ncol=**
>>> length(missing.meta.cols))
>>>
>>>> old.meta<-as.data.frame(**values(a.grs))
>>>>> new.meta<-cbind(old.meta,**extra.blank)
>>>>> values(a.grs)<-new.meta
>>>>>
>>>>
>>>> Using vanilla GenomicRanges functionality, you just do this:
>>>>
>>>> R>  values(a.grs)<- cbind(values(a.grs), DataFrame(extra.blank))
>>>>
>>>> HTH,
>>>>
>>>> -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<http://cbio.mskcc.org/%7Elianos/contact>
>>>>
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>>
>>
>>
>
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> Computational Biology
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