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
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