On Fri, Aug 27, 2010 at 7:02 AM, Martin Morgan <mtmorgan@fhcrc.org> wrote:

> On 08/27/2010 03:03 AM, Tim Yates wrote:
> > Hi Richard,
> >
> > Ahhh..cool, yeah that works. Shame it's not a unified interface across
> all
> > three datatypes though.
>
> These were intentional design decisions to reduce ambiguities in which
> of the components of these complex arguments subscript operations were
> meant to apply, in the long run making it easier to write unambiguous
> and easy to read code. Martin
>
>
I would argue that in the long run, after the user reads the documentation
and understood the API, it would result in terser code that is easier to
read and write. I think that using $ and [[ to access metadata columns is
very intuitive.

eSet does this with '$' and the phenoData right?


> >
> > Thanks for pointing me in the right direction though :-)
> >
> > Tim
> >
> > On 27/08/2010 10:31, "Richard Pearson" <richard.pearson@well.ox.ac.uk>
> > wrote:
> >
> >> Hi Tim
> >>
> >> I think you need the values accessor method here:
> >>
> >> print( values(my.gr)[[ 'name' ]] )
> >>
> >> Cheers
> >>
> >> Richard
> >>
> >>
> >> Tim Yates wrote:
> >>> Hi all,
> >>>
> >>> I'm trying to move to using GRanges objects for storing my genomic
> features
> >>> rather than IRanges objects that I use currently.
> >>>
> >>> However, I cannot seem to subscript the Genomic Ranges object to
> extract a
> >>> single column from the meta-data of the object.
> >>>
> >>> Hopefully this code explains what I am trying to do, and someone can
> point
> >>> me in the right direction?
> >>>
> >>> Cheers,
> >>>
> >>> Tim
> >>>
> >>>> library(GenomicRanges)
> >>> Loading required package: IRanges
> >>>
> >>> Attaching package: 'IRanges'
> >>>
> >>>
> >>>     The following object(s) are masked from package:base :
> >>>
> >>>      cbind,
> >>>      Map,
> >>>      mapply,
> >>>      order,
> >>>      paste,
> >>>      pmax,
> >>>      pmax.int,
> >>>      pmin,
> >>>      pmin.int,
> >>>      rbind,
> >>>      rep.int,
> >>>      table
> >>>
> >>>> library(GenomicRanges)
> >>>> my.starts  = c(     10,    100,   1000 )
> >>>> my.ends    = c(     20,    200,   2000 )
> >>>> my.spaces  = c(    '1',    '2',    '3' )
> >>>> my.strands = c(    '+',    '+',    '-' )
> >>>> my.names   = c( 'seq1', 'seq2', 'seq3' )
> >>>> my.delta   = c(   1.23,   2.34,   3.45 )
> >>>>
> >>>> my.df = data.frame( start=my.starts, end=my.ends, space=my.spaces,
> >>> strand=my.strands, name=my.names, delta=my.delta )
> >>>> my.rd = as( my.df, 'RangedData' )
> >>>> my.gr = as( my.rd, 'GRanges' )
> >>>>
> >>>
> >>> # Extract the name field from each of these objects using [[
> >>>
> >>>> print( my.df[[ 'name' ]] )
> >>> [1] seq1 seq2 seq3
> >>> Levels: seq1 seq2 seq3
> >>>> print( my.rd[[ 'name' ]] )
> >>> [1] seq1 seq2 seq3
> >>> Levels: seq1 seq2 seq3
> >>>> print( my.gr[[ 'name' ]] )
> >>> Error in my.gr[["name"]] : missing '[[' method for Sequence class
> GRanges
> >>>
> >>> # Extract the name field from each of these objects using $
> >>>
> >>>> print( my.df$'name' )
> >>> [1] seq1 seq2 seq3
> >>> Levels: seq1 seq2 seq3
> >>>> print( my.rd$'name' )
> >>> [1] seq1 seq2 seq3
> >>> Levels: seq1 seq2 seq3
> >>>> print( my.gr$'name' )
> >>> Error in x[[name, exact = FALSE]] :
> >>>   missing '[[' method for Sequence class GRanges
> >>>> sessionInfo()
> >>> R version 2.10.1 (2009-12-14)
> >>> x86_64-apple-darwin9.8.0
> >>>
> >>> locale:
> >>> [1] en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8
> >>>
> >>> attached base packages:
> >>> [1] stats     graphics  grDevices utils     datasets  methods   base
> >>>
> >>> other attached packages:
> >>> [1] GenomicRanges_1.0.8 IRanges_1.6.15
> >>> --------------------------------------------------------
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> u...{{dropped:15}}
> >>>
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