## File: extract.breakpoints.Rd

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r-cran-seqinr 3.4-5-2
 12345678910111213141516171819202122232425262728293031323334353637383940414243444546474849505152535455565758596061626364656667686970717273747576777879808182838485868788899091 \name{extract.breakpoints} \alias{extract.breakpoints} \title{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{ \item{rearr.ori}{A data frame obtained with the \code{rearranged.oriloc} function. } \item{type}{The type of skew for which to extract the breakpoints; must be a subset of \code{c("atfw","atrev","gcfw","gcrev")}.} \item{nbreaks}{The number of breakpoints to extract for each type of skew. Provide a vector of the same length as \code{type}.} \item{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 \code{gridsize} times, with different starting values for the breakpoints. } \item{it.max}{The maximum number of iterations to be performed when searching for the breakpoints. This argument corresponds to the \code{it.max} argument in \code{segmented}.} } \details{ This method uses the \code{segmented} function in the \code{segmented} package to extract the breakpoints positions in the rearranged nucleotide skews obtained with the \code{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 \code{gridsize} times, with different starting values for the breakpoints. } \value{ This function returns a list, with as many elements as the \code{type} argument (for example \code{$gcfw} will contain the results for the rearranged GC-skew, for forward-encoded genes). Each element of this list is also a list, containing the following information: in \code{$breaks} the position of the breakpoints on the rearranged chromosome; in \code{$slopes.left} the slopes of the segments on the left side of each breakpoint; in \code{$slopes.right} the slopes of the segments on the right side of each breakpoint; in \code{$real.coord}, the coordinates of the breakpoints on the real chromosome (before rearrangement). } \references{ \code{citation("segmented")} Necşulea, A. and Lobry, J.R. (in prep) A novel method for assessing the effect of replication on DNA base composition asymmetry. \emph{Molecular Biology and Evolution},\bold{24}:2169-2179. } \author{A. Necşulea} \seealso{ \code{\link{oriloc}}, \code{\link{draw.rearranged.oriloc}}, \code{\link{rearranged.oriloc}} } \examples{ ### Example for Chlamydia trachomatis #### ### Rearrange the chromosome and compute the nucleotide skews ### \dontrun{r.ori <- rearranged.oriloc(seq.fasta = system.file("sequences/ct.fasta.gz", package = "seqinr"), g2.coord = system.file("sequences/ct.coord",package = "seqinr"))} ### Extract the breakpoints for the rearranged nucleotide skews ### \dontrun{breaks <- extract.breakpoints(r.ori,type = c("gcfw", "gcrev"), nbreaks = c(2, 2), gridsize = 50, it.max = 100)} ### Draw the rearranged nucleotide skews and ### ### place the position of the breakpoints on the graphics ### \dontrun{draw.rearranged.oriloc(r.ori, breaks.gcfw = breaks$gcfw$breaks, breaks.gcrev = breaks$gcrev\$breaks)} } \keyword{utilities}