+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
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
> 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
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@r-project.org
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> > Search the archives:
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> >
>
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>



-- 
Tengfei Yin
MCDB PhD student
1620 Howe Hall, 2274,
Iowa State University
Ames, IA,50011-2274
Homepage: www.tengfei.name

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