Tim Triche, Jr. | 5 Dec 03:55 2012
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Re: table for GenomicRanges

What would its output look like?

Certainly you can do it with the metadata columns:

R> segmentation(AML200)$CD14_MONO
GRanges with 619643 ranges and 1 metadata column:
           seqnames               ranges strand   |             state
              <Rle>            <IRanges>  <Rle>   |          <factor>
       [1]     chr1       [    1,  9800]      *   |         Quiescent
       [2]     chr1       [ 9801, 10800]      *   |         Quiescent
       [3]     chr1       [10801, 11000]      *   |         Quiescent
       [4]     chr1       [11001, 12200]      *   |              CTCF
       ...      ...                    ...    ... ...               ...

R> table(segmentation(AML200)$CD14_MONO$state)

   StrongEnhancer      WeakEnhancer    PoisedPromoter PolycombRepressed
            65990             74465             18219             52787
        Quiescent     Transcription        Elongation              CTCF
           176451             79811             59474             29116
   StrongPromoter      WeakPromoter    ActivePromoter
            31322             19628             37694

But I assume that is not what you are after.

On Tue, Dec 4, 2012 at 4:25 PM, Vedran Franke <vfranke@...> wrote:

> Dear All,
>
> Is there an equivalent of the table function for a GenomicRanges object?
>
> Best,
>
> Vedran
>
>
> --
> Vedran Franke
>
> Bioinformatics Group,
> Department of Molecular Biology,
> Faculty of Science, Zagreb
>
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--

-- 
*A model is a lie that helps you see the truth.*
*
*
Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>

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