[BioC] GRangesList filtering

[Valerie Obenchain]

Hi Halian,

   gr1 <- GRanges(seqnames = "chr2", ranges = IRanges(3, 6))
   gr2 <- GRanges(seqnames = c("chr1", "chr1"), ranges = 
IRanges(c(7,13), width = 3))
   gr3 <- GRanges(seqnames = c("chr1", "chr2"), ranges = IRanges(c(1, 
4), c(3, 9)))
   grl <- GRangesList("gr1" = gr1, "gr2" = gr2, "gr3" = gr3)

   grl[seqnames(grl) == "chr2"]

Valerie


On 05/01/2012 07:26 AM, Halian Vilela wrote:
> Hey guys,
>
> I would like to know if there are any methods of efficiently subset a
> GRangeList by it seqnames.
>
> I have something like this:
>
>
> GRangesList of length 86046:
> $1
> GRanges with 27 ranges and 3 elementMetadata values:
>         seqnames               ranges strand   |   exon_id   exon_name exon_rank
>            <Rle>             <IRanges>   <Rle>    |<integer>  <character>  <integer>
>     [1]     chr1 [66999065, 66999090]      +   |         1<NA>          1
>     [2]     chr1 [66999928, 67000051]      +   |         2<NA>          2
>     [3]     chr1 [67091529, 67091593]      +   |         3<NA>          3
>     [4]     chr1 [67098752, 67098777]      +   |         4<NA>          4
>     [5]     chr1 [67099762, 67099846]      +   |         5<NA>          5
>     [6]     chr1 [67105459, 67105516]      +   |         6<NA>          6
>     [7]     chr1 [67108492, 67108547]      +   |         7<NA>          7
>     [8]     chr1 [67109226, 67109402]      +   |         8<NA>          8
>     [9]     chr1 [67126195, 67126207]      +   |         9<NA>          9
>     ...      ...                  ...    ... ...       ...         ...       ...
>
>
>
> In which each element ($1,$2,$3,...) represents a transcript and it
> set of exons...
>
> In the seqnames colum I have the chromosomes ranging from 1 to Y (all
> 24 human cromosomes), what I would like to know is how to get just the
> elements accounting for chromosome 14...
>
> I have made successfully by unlisting the structure into a huge normal
> GRange and then subseting normally:
>
> ex<- unlist(ex_tx)
> ex14<- ex[which(seqnames(ex) == "chr14")]
>
>
> But obviously I lose the GRangesList structure. So are there any way
> to subset this directly in the GRangesList without the need to unlist,
> in a way that my result is also a GRangesList ?
>
> Thanks,
> Halian
>
> 	[[alternative HTML version deleted]]
>
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