[BioC] Subscripting GenomicRanges objects with [[ or $

[Tim Yates]

Hi again,

One of the really nice things about the RangedData object is that it could
be treated (in general) the same way you would treat a data.frame, so it was
possible to write methods that handled both object types the same way.

I have a method which currently accepts a data.frame or a RangedData object
which I want to extend to allowing GRanges objects as well

Without the [[ or $ subscript operators being implemented would I need to
have a switch based on the class of the parameter?

As the values(obj)[['field']] method only works for GRanges objects (for
RangedData, this method does not cause an error, it just returns NULL), I
guess I would need to write something like this:

.get.column = function( obj, field ) {
      if( class( obj ) == 'GRanges' ) {
          values(obj)[[ field ]]
      }
      else {
          obj[[ field ]]
      }
    }

Then, call

  .get.column(obj,'name')

wherever I used to simply use

  obj[['name']]

before introducing GenomicRanges?

Tim

On 27/08/2010 15:02, "Martin Morgan" <mtmorgan at 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
> 
>> 
>> Thanks for pointing me in the right direction though :-)
>> 
>> Tim
>> 
>> On 27/08/2010 10:31, "Richard Pearson" <richard.pearson at 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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