[BioC] Subscripting GenomicRanges objects with [[ or $
Richard Pearson
richard.pearson at well.ox.ac.uk
Fri Aug 27 11:31:26 CEST 2010
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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--
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
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