That would be great. Smoothing is a very common manipulation of a wig file.
Thank you all. Ivan Ivan Gregoretti, PhD National Institute of Diabetes and Digestive and Kidney Diseases National Institutes of Health 5 Memorial Dr, Building 5, Room 205. Bethesda, MD 20892. USA. Phone: 1-301-496-1592 Fax: 1-301-496-9878 On Thu, Jul 23, 2009 at 2:35 PM, Patrick Aboyoun<[email protected]> wrote: > I haven't started down this road yet, but I could add 1D smoothers for Rle > objects. Then you can convert the RangedData objects to Rle objects and run > smoothers over them. > > > Patrick > > > > Michael Lawrence wrote: >> >> On Thu, Jul 23, 2009 at 11:06 AM, Simon Anders <[email protected]> wrote: >> >> >>> >>> Michael Lawrence wrote: >>> >>>> >>>> Oops, I meant: >>>> y <- rep(score(chr1), width(chr1)) >>>> >>>> >>>> >>>>> >>>>> x <- as.integer(unlist(ranges(chr1))) >>>>> lo <- loess(y ~ x) >>>>> >>> >>> But what if the intervals in the wiggle file contain gaps? That's >>> perfectly legal, after all. >>> >>> >> >> This is what the as.integer(...) is handling. 'x' will contain the actual >> position of each value in 'y'. >> >> >> >>> >>> I also fail to see what the effect of as.integer on IRanges is supposed >>> to be. For my wiggle file, I simply get >>> >>> >>>> >>>> head( as.integer( unlist( ranges(w) ) ) ) >>>> >>> >>> [1] 2 3 4 5 6 7 >>> >>> >> >> It's like calling seq(start, end) on each range in the IRanges and >> concatenating the result. >> >> It could be implemented as: >> do.call("c", lapply(seq_along(chr1), function(i) seq(start(chr1)[i], >> end(chr1)[i]))) >> >> But it's actually implemented in compiled code and is very fast. >> >> >>> >>> ir <- IRanges(c(5, 12), c(10, 15)) >>> as.integer(ir) >>> >> >> [1] 5 6 7 8 9 10 12 13 14 15 >> >> >> >>> >>> Simon >>> >>> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioc-sig-sequencing mailing list >> [email protected] >> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing >> > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
