On Thu, Jul 23, 2009 at 10:59 AM, Michael Lawrence <[email protected]>wrote:
> > > On Thu, Jul 23, 2009 at 10:45 AM, Simon Anders <[email protected]> wrote: > >> Hi Michael >> >> Michael Lawrence wrote: >> > Well, to get the scores: >> > >> > track <- import("foo.wig") >> > scores <- score(track) >> > >> > Now you are free to use any of the functions in R for smoothing a >> numeric >> > vector. Like loess(), runmed(), etc. >> >> Careful! This does not work, as you ignore the ranges. >> > > Thanks for pointing that out. One easy way is to just get the 'x' variable, > as in: > > chr1 <- track["chr1"] # limit to single chromosome > y <- score(chr1) > Oops, I meant: y <- rep(score(chr1), width(chr1)) > > x <- as.integer(unlist(ranges(chr1))) > lo <- loess(y ~ x) > > Michael > > >> Take, for example, this wiggle file here, which starts with: >> >> track type=wiggle_0 name="coverage 06-GL3" >> 06 1 40128 0 >> 06 40128 40164 0.881 >> 06 40164 40245 0 >> 06 40245 40257 0.881 >> 06 40257 40281 1.444 >> [...] >> >> Observe: >> >> > w <- import( "igb/06-GL3-coverage.wig" ) >> > s <- score( w ) >> > str(s) >> num [1:338864] 0 0.881 0 0.881 1.444 ... >> >> The score vector 's' should start with 40127 times a '0' but we have >> only a single 0. >> >> >> Simon >> > > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
