Hi Andrew -- On 06/23/2010 02:02 PM, Andrew Yee wrote: > Hi, I'm trying to figure out the coverage for a specific range. > > Take for example, > > r <- IRanges(start = c(30, 60, 70, 100), width = c(20, 18, 20, 18)) > > I'm interested in the coverage from positions 60 to 65, which in this case > is 1. I'm also interested in the coverage say from positions 68 to 73, > which goes from 1 to 2. > > While I can use coverage(r) and then use runLength() and runValue() to > ultimately extract this information, is there a way to use coverage so that > you can directly specify the positions of interest?
One possibility is to create views onto your coverage vector r <- IRanges(start = c(30, 60, 70, 100), width = c(20, 18, 20, 18)) roi = IRanges(c(60, 68), width=5) ## 'regions of interest' v = Views(coverage(r), roi) and then do all sorts of fun things, like home movies for (i in seq_len(length(v))) plot(as.integer(v[[i]]), type="l") Martin > > Thanks, > Andrew > >> sessionInfo() > R version 2.11.0 (2010-04-22) > x86_64-unknown-linux-gnu > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] IRanges_1.6.0 > > loaded via a namespace (and not attached): > [1] tools_2.11.0 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793 _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
