Hi Patrick,
It worked very well and extremely fast, that's exactly what I was looking
for. Now I have another question, how do I use the RleViewsList I created to
calculate basewise coverage? I was trying to get help from the document but
did not find anything. 
 
Thanks,
Xiaojun

  _____  

From: Patrick Aboyoun [mailto:paboyoun@fhcrc.org] 
Sent: Thursday, June 17, 2010 12:30 AM
To: Di, Xiaojun; bioc-sig-sequencing@r-project.org
Subject: Re: questions on Coverage function and IRanges package


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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