Xiaojun Di,
I am responding to your question on the BioC-SIG-Seq mailing list since 
this question may be of interest to others. The answer is yes, you can 
find out the coverage within exonic regions. See the help for the 
RleViewsList class for more information. The steps would be

1) Create the coverage across the genome.
2) Use the RleViewsList function to limit your "view" to the exonic 
locations.
3) (Optional) Use viewMaxs/viewSums/viewMeans to summarize each of the 
exonic locations.


Alternatively, you can use the countOverlaps functions to count to the 
number of alignments that "hit" each of the exonic locations.


Cheers,

Patrick



On 6/16/10 12:54 PM, Di, Xiaojun wrote:
> Hi Patrick,
> I am trying to get familar with IRanges, ShortRead and other 
> NGS-related packages. I have a very simple problem I want to solve 
> which I can solve but not very smartly, hope you have a better way.
> Here is the problem:
> I have human exome data which is already aligned to whole human exons, 
> but with 200bp extension to both ends of each exon. I can get the 
> coverage directly for the whole extended sequence by calling function 
> coverage, but what I really want is the coverage on the bases 
> within exons without the extensions, do you have a function to do that?
> Thanks,
> Xiaojun Di
> Covance Genomics Lab
> Seattle, WA
>
>
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