### Example for Chlamydia trachomatis ####
### Rearrange the chromosome and compute the nucleotide skews ###
## Not run: r.ori <- rearranged.oriloc(seq.fasta =
# system.file("sequences/ct.fasta.gz", package = "seqinr"),
# g2.coord = system.file("sequences/ct.predict", package = "seqinr"))## End(Not run)
### Extract the breakpoints for the rearranged nucleotide skews ###
## Not run: breaks <- extract.breakpoints(r.ori, type = c("gcfw", "gcrev"),
# nbreaks =c(2, 2), gridsize = 50, it.max = 100)## End(Not run)
### Draw the rearranged nucleotide skews and place the position of the breakpoints ###
### on the graphics ###
## Not run: draw.rearranged.oriloc(r.ori, breaks.gcfw = breaks$gcfw$breaks,
# breaks.gcrev = breaks$gcrev$breaks)## End(Not run)
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