Generally, people summarize the coverage in each island, like with viewSums,
viewMaxs, etc. For other, custom summaries, see viewApply (but this is not
optimized like the others).

Michael

On Thu, Apr 14, 2011 at 7:19 AM, Lakshmanan Iyer <laxvid@gmail.com> wrote:

> Hi
> I have calculated coverage and islands of coverage from a filtered set of
> alignments from a bam file using Bioconductor tools. I finally got the
> islands but am stuck with how to extract the individual coverage at each
> position on the islands. Any help is appreciated. Details below:
> .....
> cov <- coverage(filtData2)
> islands <- slice (cov, lower=1);
> ....
>
> > islands
> SimpleRleViewsList of length 22
> $chr1
> Views on a 196923949-length Rle subject
>
> views:
>           start       end width
>   [1]   3204937   3205007    71 [1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
> ...]
>   [2]   3205421   3205491    71 [1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
> ...]
>   [3]   4886462   4886532    71 [1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
> ...]
>   [4]   4887255   4887325    71 [1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
> ...]
>   [5]   6849632   6849852   221 [1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2
> ...]
>   [6]   7160418   7160488    71 [1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
> ...]
>   [7]   7160629   7160699    71 [1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
> ...]
>   [8]   7160746   7160816    71 [1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
> ...]
>   [9]   7160832   7160902    71 [1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
> ...]
>   ...       ...       ...   ... ...
> [1186] 196640431 196640663   233 [ 1  1  1  2  4  4  4  5  5  5  5  5  5
> ...]
> [1187] 196640859 196641155   297 [3 5 5 6 6 7 7 7 7 7 7 7 7 7 8 8 8 8 8 8
> ...]
> [1188] 196641193 196641265    73 [1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
> ...]
>
> I was wondering how one could get the coverage values out of this
> SimpleRleViewsList (see below)
> I could get the dataframe and he named columns, see
>
>  space   start     end width
> 1  chr1 3204937 3205007    71
> 2  chr1 3205421 3205491    71
> 3  chr1 4886462 4886532    71
>
> but would like to get the coverage at each position so that I can use it do
> some more analysis
>
> [1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ...]
>
> Any clues?
> -best
> -Lax
>
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>
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