Jim,
Have you tried letterFrequencyInSlidingView in Biostrings?
> library(Biostrings)
> data(phiX174Phage)
> dna <- phiX174Phage[[1]]
> class(dna)
[1] "DNAString"
attr(,"package")
[1] "Biostrings"
> args(letterFrequencyInSlidingView)
function (x, view.width, letters, OR = "|")
NULL
> head(letterFrequencyInSlidingView(dna, 2, DNA_BASES))
A C G T
[1,] 1 0 1 0
[2,] 1 0 1 0
[3,] 0 0 1 1
[4,] 0 0 0 2
[5,] 0 0 0 2
[6,] 0 0 0 2
> sessionInfo()
R version 2.11.1 Patched (2010-05-31 r52167)
i386-apple-darwin9.8.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] Biostrings_2.16.5 IRanges_1.6.8
loaded via a namespace (and not attached):
[1] Biobase_2.8.0 tools_2.11.1
Patrick
On 6/21/10 4:56 PM, James Bullard wrote:
Hi,
This must be readily doable and I am just missing the obvious -- I am
trying, for a long sequence, to classify each position as coming from a
particular context. Something like running nucleotide table. The things
that I have thought about doing are:
.) Making Views representing my sliding windows, but then I don't see an
obvious thing except nucleotide frequency, but that doesn't really solve
the problem.
.) Using nucleotideFrequencyAt, however, I am not sure that this function
does what I want. Since it takes an XStringSet type object rather than a
DNAString type object.
thanks, jim
_______________________________________________
Bioc-sig-sequencing mailing list
[email protected]
https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
_______________________________________________
Bioc-sig-sequencing mailing list
[email protected]
https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
