seqinr: permutation – R documentation

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permutation

Sequence permutation according to several different models

Description

Generates a random permutation of a given sequence, according to a given model. Available models are : base, position, codon, syncodon.

Usage

permutation(sequence,modele='base',frame=0,
 replace=FALSE,prot=FALSE,numcode=1,ucoweight = NULL)

Arguments

`sequence`	A nucleic acids sequence
`modele`	A string of characters describing the model chosen for the random generation
`frame`	Only active for the `position`, `codon`, `syncodon` models: starting position of CDS as in `splitseq`
`replace`	This option is not active for the `syncodon` model: if `TRUE`, sampling is done with replacement
`prot`	Only available for the `codon` model: if `TRUE`, the first and last codons are preserved, and only intern codons are shuffled
`numcode`	Only available for the `syncodon` model: the genetic code number as in `translate`.
`ucoweight`	A list of weights containing the desired codon usage bias as generated by `ucoweight`. If none is specified, the codon usage of the given sequence is used.

Details

The base model allows for random sequence generation by shuffling (with/without replacement) of all bases in the sequence.

The 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 codon model allows for random sequence generation by shuffling (with/without replacement) of codons.

The syncodon model allows for random sequence generation by shuffling (with/without replacement) of synonymous codons.

Value

a sequence generated from the original one by a given model

Author(s)

L. Palmeira

References

citation("seqinr")

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)

seqinr

Biological Sequences Retrieval and Analysis

v4.2-16

GPL (>= 2)

Authors

Delphine Charif [aut], Olivier Clerc [ctb], Carolin Frank [ctb], Jean R. Lobry [aut, cph], Anamaria Necşulea [ctb], Leonor Palmeira [ctb], Simon Penel [cre], Guy Perrière [ctb]

Initial release

2022-05-19