R: Graphical representation for rearranged nucleotide skews in...

draw.rearranged.oriloc {seqinr} | R Documentation

## Graphical representation for rearranged nucleotide skews in prokaryotic chromosomes.

### Description

Graphical representation for rearranged nucleotide skews in prokaryotic chromosomes.

### Usage

    draw.rearranged.oriloc(rearr.ori, breaks.gcfw = NA,
     breaks.gcrev = NA, breaks.atfw = NA, breaks.atrev = NA)

### Arguments

`rearr.ori` | A data frame obtained with the `rearranged.oriloc` function.
`breaks.gcfw` | The coordinates of the breakpoints in the GC-skew, for forward transcribed protein coding sequences. These coordinates can be obtained with the `extract.breakpoints` function.
`breaks.gcrev` | The coordinates of the breakpoints in the GC-skew, for reverse transcribed protein coding sequences. These coordinates can be obtained with the `extract.breakpoints` function.
`breaks.atfw` | The coordinates of the breakpoints in the AT-skew, for forward transcribed protein coding sequences. These coordinates can be obtained with the `extract.breakpoints` function.
`breaks.atrev` | The coordinates of the breakpoints in the AT-skew, for reverse transcribed protein coding sequences. These coordinates can be obtained with the `extract.breakpoints` function.

### Author(s)

J.R. Lobry, A. Necşulea

### References

Necşulea, A. and Lobry, J.R. (2007) A New Method for Assessing the Effect of Replication on DNA Base Composition Asymmetry. Molecular Biology and Evolution, 24:2169-2179.

### See Also

`rearranged.oriloc`, `extract.breakpoints`

### Examples

    ## 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)

[Package seqinr version 3.4-5 Index]