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