[BioC] Subscripting GenomicRanges objects with [[ or $

[Tim Yates]

Hi Richard,

Ahhh..cool, yeah that works. Shame it's not a unified interface across all
three datatypes though.

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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