[BioC] autocorrelation analysis

[mattia pelizzola]

Hi,

I am trying to get some autocorrelation analysis based on positions of
DNA words. Given a certain DNA motif or word, you can have its
positions on the genome. I am trying to figure out if there is any
regularity (pattern) in that. What I did is to determine pair-wise
distances and see how many pairs have a certain distance. The result
indicates that is more likely to have such words at a given relative
distance than at others, but it is not so easy to interpret. Is there
any way to test this? There is a lot of functions in R about testing
autocorrelation on time-series data or 2D geographical data .. but
these do not seem really appropriate here to me.
Also, it would be nice to test weather two positions sets for two
different motifs are correlated ..

thanks for any suggestion!

mattia