## File: permutation.Rd

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r-cran-seqinr 3.4-5-2
 12345678910111213141516171819202122232425262728293031323334353637383940414243444546474849505152535455565758596061626364656667 \name{permutation} \alias{permutation} \title{Sequence permutation according to several different models} \description{ Generates a random permutation of a given sequence, according to a given model. Available models are : \code{base}, \code{position}, \code{codon}, \code{syncodon}. } \usage{permutation(sequence,modele='base',frame=0, replace=FALSE,prot=FALSE,numcode=1,ucoweight = NULL)} \arguments{ \item{sequence}{ A nucleic acids sequence } \item{modele}{ A string of characters describing the model chosen for the random generation } \item{frame}{ Only active for the \code{position}, \code{codon}, \code{syncodon} models: starting position of CDS as in \code{splitseq} } \item{replace}{ This option is not active for the \code{syncodon} model: if \code{TRUE}, sampling is done with replacement } \item{prot}{ Only available for the \code{codon} model: if \code{TRUE}, the first and last codons are preserved, and only intern codons are shuffled } \item{numcode}{ Only available for the \code{syncodon} model: the genetic code number as in \code{translate}. } \item{ucoweight}{ A list of weights containing the desired codon usage bias as generated by \code{ucoweight}. If none is specified, the codon usage of the given sequence is used. } } \value{ a sequence generated from the original one by a given model } \details{ The \code{base} model allows for random sequence generation by shuffling (with/without replacement) of all bases in the sequence. The \code{position} model allows for random sequence generation by shuffling (with/without replacement) of bases within their position in the codon (bases in position I, II or III stay in position I, II or III in the new sequence. The \code{codon} model allows for random sequence generation by shuffling (with/without replacement) of codons. The \code{syncodon} model allows for random sequence generation by shuffling (with/without replacement) of synonymous codons. } \references{ \code{citation("seqinr")} } \author{L. Palmeira} \seealso{ \code{\link{synsequence}} } \examples{ data(ec999) sequence=ec999[1][[1]] new=permutation(sequence,modele='base') identical(all.equal(count(new,1),count(sequence,1)),TRUE) new=permutation(sequence,modele='position') identical(all.equal(GC(new),GC(sequence)),TRUE) identical(all.equal(GC2(new),GC2(sequence)),TRUE) identical(all.equal(GC3(new),GC3(sequence)),TRUE) new=permutation(sequence,modele='codon') identical(all.equal(uco(new),uco(sequence)),TRUE) new=permutation(sequence,modele='syncodon',numcode=1) identical(all.equal(translate(new),translate(sequence)),TRUE) } \keyword{ utilities }