[Bioc-sig-seq] more operations on BamViews

[Martin Morgan]

On 03/01/2011 04:44 AM, Michael Lawrence wrote:
> Hi guys,
> 
> What are the plans for the BamViews class. It looks like a useful
> foundation. One thing that would be good to have in R is a way to calculate
> "pileups" or base tallies for positions of interest. These counts could be
> broken down by sample (bamfile), cycle (position in the read), etc. Results
> returned as a DataFrame (in a format like that returned by as.data.frame on
> a table) that could be aggregated() up as desired. Rles would save memory.
> So there could be something like a alphabetFrequency() method for BamViews.
> This is related to Steve's recent work with counting over XStringSets.

Hi Michael -- BamViews is definitely open for more development. The
methods currently implemented (minimal!) basically dispatch to
single-bam variants. And I guess there is no single-bam variant of what
you're looking for.

Another possibility is to expose more of samtools, e.g., pileup /
mpileup, which might be returned more or less directly for manipulation
in R, or summarized. I'll work on this in the 3 week time frame (sorry)

Maybe Herve will weigh in on Steve's XStringSet sliding window
letterFrequencyAt

Martin

> 
> Surely there are many other features that could be added. The above is just
> one that I would use often, across a number of contexts.
> 
> Thanks,
> Michael
> 
> 	[[alternative HTML version deleted]]
> 
> _______________________________________________
> Bioc-sig-sequencing mailing list
> Bioc-sig-sequencing at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing


-- 
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109

Location: M1-B861
Telephone: 206 667-2793