[Bioc-sig-seq] smoothing techniques

[Patrick Aboyoun]

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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