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) [[alternative HTML version deleted]] ______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
