[BioC] Subscripting GenomicRanges objects with [[ or $

[Richard Pearson]

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 
> --------------------------------------------------------
> This email is confidential and intended solely for the u...{{dropped:15}}
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
> 

-- 
Dr Richard D Pearson                       richard.pearson at well.ox.ac.uk
Wellcome Trust Centre for Human Genetics   http://www.well.ox.ac.uk/~rpearson
University of Oxford                       Tel: +44 (0)1865 617890
Roosevelt Drive                            Mob: +44 (0)7971 221181
Oxford OX3 7BN, UK                         Fax: +44 (0)1865 287664