seqinr (version 1.0-1)

uco: Create codon usage table

Description

uco calculates some codon usage index: the codon count eff, the absolute frequencies freq or the Relative Synonymous Codon Usage rscu.

Usage

uco( seq, frame = 0, index = c("eff","freq","rscu"), as.data.frame = FALSE)

Arguments

seq

a vector of chars

frame

an integer (0,1,2) giving the frame

index

One of this value

as.data.frame

logical. If TRUE: The eff, freq and rscu index will be returned in a data frame.

Value

• If as.data.frame is TRUE uco returns a data frame with five columns:
• aa
  a vector containing the name of amino-acid
• codon
  a vector containing the corresponding codon
• eff
  a numeric vector containing effectifs of codons
• freq
  a numeric vector containing frequencies of codons
• rscu
  a numeric vector containing the relative synonymous codon usage
• If as.data.frame is FALSE, uco returns one of this index:
• eff
  a factor containing effectifs of codons
• freq
  a factor containing frequencies of codons
• rscu
  a factor containing the relative synonymous codon usage

References

� To have an overview of the seqinR's functionnality, please consult this vignette: Charif, D., Lobry, J.R. (2005) SeqinR: a contributed package to the R project for statistical computing devoted to biological sequences retrieval and analysis. Springer Verlag, Biological and Medical Physics/Biomedical Series, in preparation.

Examples

s = read.fasta(File=system.file("sequences/malM.fasta",package = "seqinr"))
uco( s[[1]], index="freq")
uco( s[[1]], index="eff")
uco( s[[1]], index="rscu")
uco( s[[1]], as.data.frame = TRUE)