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)
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
>
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