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 > [email protected] > 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 _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
