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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