Herve, thanks for your help. To follow up some more, is there a way to directly specify the start and end in coverage(), without using shift and width?
Or alternatively, as Martin suggests, 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) but in this case, extract the coverage information from v in the above example? Thanks, Andrew 2010/6/25 Hervé Pagès <[email protected]> > Hi Andrew, > > One way to specify directly the window of interest when calling > coverage() is to use the 'shift' and 'width' arguments. > 'shift' allows you to shift the ranges contained in the first > argument to the left (negative shift) or to the right (positive > shift) before extracting the coverage: > > ## Coverage from positions 60 to 65: > > as.integer(coverage(r, shift=-59, width=6)) > [1] 1 1 1 1 1 1 > > ## Coverage from positions 68 to 73: > > as.integer(coverage(r, shift=-67, width=6)) > [1] 1 1 2 2 2 2 > > Note that coverage(r, shift=-59, width=6) is equivalent to > coverage(shift(r, -59), width=6). > > Cheers, > H. > > > > 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? >> >> 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 >> > > [[alternative HTML version deleted]]
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