R: Extraction of breakpoint positions on the rearranged...

extract.breakpoints {seqinr} | R Documentation

## Extraction of breakpoint positions on the rearranged nucleotide skews.

### Description

Extraction of breakpoint positions on the rearranged nucleotide skews.

### Usage

    extract.breakpoints(rearr.ori,
    type = c("atfw", "atrev", "gcfw", "gcrev"),
     nbreaks, gridsize = 100, it.max = 500)

### Arguments

`rearr.ori` | A data frame obtained with the `rearranged.oriloc` function.
`type` | The type of skew for which to extract the breakpoints; must be a subset of `c("atfw","atrev","gcfw","gcrev")`.
`nbreaks` | The number of breakpoints to extract for each type of skew. Provide a vector of the same length as `type`.
`gridsize` | To make sure that the best breakpoints are found, and to avoid finding only a local extremum of the likelihood and residual sum of square functions, a grid search is performed. The search for breakpoints is repeated `gridsize` times, with different starting values for the breakpoints.
`it.max` | The maximum number of iterations to be performed when searching for the breakpoints. This argument corresponds to the `it.max` argument in `segmented`.

### Details

This method uses the `segmented` function in the `segmented` package to extract the breakpoints positions in the rearranged nucleotide skews obtained with the `rearranged.oriloc` function. To make sure that the best breakpoints are found, and to avoid finding only a local extremum of the likelihood and residual sum of square functions, a grid search is performed. The search for breakpoints is repeated `gridsize` times, with different starting values for the breakpoints.

### Value

This function returns a list, with as many elements as the `type` argument (for example `$gcfw` will contain the results for the rearranged GC-skew, for forward-encoded genes). Each element of this list is also a list, containing the following information: in `$breaks` the position of the breakpoints on the rearranged chromosome; in `$slopes.left` the slopes of the segments on the left side of each breakpoint; in `$slopes.right` the slopes of the segments on the right side of each breakpoint; in `$real.coord`, the coordinates of the breakpoints on the real chromosome (before rearrangement).

### Author(s)

A. Necşulea

### References

`citation("segmented")`

Necşulea, A. and Lobry, J.R. (in prep) A novel method for assessing the effect of replication on DNA base composition asymmetry. Molecular Biology and Evolution,24:2169-2179.

### See Also

`oriloc`, `draw.rearranged.oriloc`, `rearranged.oriloc`

### Examples

    ### 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.coord",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)

[Package seqinr version 3.4-5 Index]