Hi all,

I just compiled package dna v. 0.2 from source and am having some  
difficulty with the window argument of the dotmatrix function.

Some test code; say I'm simulating some nucleotide sequences:

   sequence1<-trunc(runif(200,0,4))
   sequence2<-trunc(runif(200,0,4))

I embed a nice 100 element alignment:

   sequence1[7:107] <- sequence2[60:160]

Plotting this with a window size of 1 produces a very dense plot  
because of the small grammar size.

   dotmatrix(rbind(sequence1, sequence2), window=1)

However, when I plot it with a larger window (generally between 6 and  
100)

   dotmatrix(rbind(sequence1, sequence2), window=10)

I get no matches (no dots).  Perhaps I'm confusing the meaning of  
"window" in this function with another type of window used to fight  
this random-match issue.  Any help would be appreciated.

Jeff.
http://www.nd.edu/~jspies/

version()
                _
platform       powerpc-apple-darwin8.7.0
arch           powerpc
os             darwin8.7.0
system         powerpc, darwin8.7.0
status
major          2
minor          4.0
year           2006
month          10
day            03
svn rev        39566
language       R
version.string R version 2.4.0 (2006-10-03)



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