[Bioc-sig-seq] Local Context

James Bullard bullard at stat.berkeley.edu
Tue Jun 22 01:56:42 CEST 2010


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



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