Bogdan,
The IRanges package (in BioC 2.5/R 2.10 and BioC 2.6/R-devel) has the
following methods for smoothing coverage vectors (stored as Rle or
RleList objects):
runsum - Running window sums
runmean - Running window means
runwtsum - Running window weighted sums (i.e. fixed kernel smoothing)
runmed - Running window medians
runq - Running window order statistics (mins, maxs, etc.)
To find out more about these functions, load the IRanges package and
type help(runmean). Here is a toy example:
> library(IRanges)
> x <- Rle(1:10)
> x
'integer' Rle of length 10 with 10 runs
Lengths: 1 1 1 1 1 1 1 1 1 1
Values : 1 2 3 4 5 6 7 8 9 10
> runmean(x, k = 5, endrule="constant")
'numeric' Rle of length 10 with 6 runs
Lengths: 3 1 1 1 1 3
Values : 3 4 5 6 7 8
> runmed(x, k = 3)
'integer' Rle of length 10 with 10 runs
Lengths: 1 1 1 1 1 1 1 1 1 1
Values : 1 2 3 4 5 6 7 8 9 10
Patrick
Bogdan Tanasa wrote:
Dear all,
please could you let me know whether any smoothing techniques (eg moving
average)
were implemented in any of the BioC packages that handle Chip-Seq/RNA-seq
data ?
thanks,
bogdan
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