Never mind, I figured out a way which is not too bad. _____
From: Di, Xiaojun Sent: Friday, June 18, 2010 3:04 PM To: 'Patrick Aboyoun'; [email protected] Subject: RE: questions on Coverage function and IRanges package 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:[email protected]] Sent: Thursday, June 17, 2010 12:30 AM To: Di, Xiaojun; [email protected] 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 ----------------------------------------------------- Confidentiality Notice: This e-mail transmission\ may co...{{dropped:19}} _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
