I'm not sure exactly what you're asking. But something like: reduce(slice(coverage(x), 2), min.gapwidth=2)
might get you close. Michael On Wed, Sep 8, 2010 at 4:34 PM, Kunbin Qu <[email protected]> wrote: > Hi, > > I have multiple IRanges separated by certain distance which I would like > to merge by REDUCE with the parameter min.gapwidth. If an IRange is > within the min.gapwidth, but the coverage is too low, say, only 1 or 2 > across, I'd like to skip it, ie, do not perform REDUCE. Could anyone > suggest a good way to do it? Thanks. > > -Kunbin > > Example like the following: > > > x<-IRanges(c(1,1,2,3,3,7,10,10,11), c(2,3,3,4,5,8,11,12,13)) > > x > IRanges of length 9 > start end width > [1] 1 2 2 > [2] 1 3 3 > [3] 2 3 2 > [4] 3 4 2 > [5] 3 5 3 > [6] 7 8 2 > [7] 10 11 2 > [8] 10 12 3 > [9] 11 13 3 > > coverage(x) > 'integer' Rle of length 13 with 12 runs > Lengths: 1 1 1 1 1 1 2 1 1 1 1 1 > Values : 2 3 4 2 1 0 1 0 2 3 2 1 > > xr<-reduce(x, min.gapwidth=2) > > xr > IRanges of length 1 > start end width > [1] 1 13 13 > > IRange No. 6 is the weak link with a coverage of 1 in the middle, but it > links IRanges 1 to 5 with IRanges 7 to 9 to cause only one IRange after > REDUCE. > > I'd like to avoid this, so REDUCE will result two clusters, one from > IRanges 1 to 5, another from IRanges 7 to 9. > > > ______________________________________________________________________ > The contents of this electronic message, including any attachments, are > intended only for the use of the individual or entity to which they are > addressed and may contain confidential information. If you are not the > intended recipient, you are hereby notified that any use, dissemination, > distribution, or copying of this message or any attachment is strictly > prohibited. If you have received this transmission in error, please send an > e-mail to [email protected] and delete this message, along with > any attachments, from your computer. > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
