if (FALSE) {
### 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)}
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