See the GenomicFeatures package and the TxDb.Hsapiens.UCSC.knownGene
package.

Then:

sum(ranges(islands3) %in%
threeUTRsByTranscript(TxDb_Hsapiens_UCSC_knownGene))

Will give you the total count over the whole genome.

Michael

On Mon, Oct 17, 2011 at 1:48 PM, rohan bareja <rohan_1925@yahoo.co.in>wrote:

> Hi,
> I am trying to get the coverage of the reads and then getting the islands
> on the basis of minimum continuous coverage.Below is my code:
> >reads <- readBamGappedAlignments("Galaxy Ctrl.bam")
> >cover=coverage(reads)
>
> >islands3 <- slice(cover, lower = 3)
> > islands3
> SimpleRleViewsList of length 93
> $chr1
> Views on a 249250621-length Rle subject
> views:            start       end width    [1]     10042     10109    68 [3
> 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 ...]    [2]     11745     11812    68 [3
> 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 ...]    [3]     14341     14489   149 [
> 3  3  3  3
>   3  3  3  3  3  3  3  3  3 ...]    [4]     16447     16524    78 [3 3 4 4
> 4 4 4 5 6 6 7 7 7 7 7 7 7 7 7 ...]    [5]     19125     19194    70 [3 3 3 3
> 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 ...]    [6]     20774     20843    70 [3 4 4 4
> 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 ...]    [7]     21283     21361    79 [ 3  3
>  3  3  3  5  7  8 10 10 10 10 10 ...]    [8]
>  21417     21497    81 [3 3 4 4 4 4 4 4 4 4 5 6 6 6 6 6 6 6 6 ...]    [9]
>   21984     22062    79 [ 3  7 13 19 29 35 40 44 45 46 46 47 47 ...]    ...
>       ...       ...   ... ...[52042] 249234021 249234091    71 [4 4 4 4 4 4
> 4 4 5 4 4 4 4 4 4 4 4 4 4 ...][52043] 249234398 249234468    71 [6 7 7 7 7 8
> 8 8 8 8 8 8 8 8 8 8 8 8 8 ...][52044] 249234596 249234658    63 [3 3 3 3 3 4
> 4 4 4 4 4 4 4 4 4 4 4 4 4
>  ...]
>
> Now,I want to get how many of these total regions (52,044 ) fall in 3'UTRs
> of chromosome 1.
> Does anybody have any idea about this?or Are there any Bioconductor
> packages that could help in similar sort of analysis?
>
> Thanks,Rohan
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>
>
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