get.ws {tAI} | R Documentation |
Relative adaptiveness values
Description
Calculates the relative adaptiveness values of codons based on the number of tRNA genes.
Usage
get.ws(tRNA, s = NULL, sking)
Arguments
tRNA |
a vector of length 64 with tRNA gene copy numbers |
s |
a vector of length 9 with selection penalties for codons |
sking |
a vector of length 1 indicating the superkingdom |
Details
The relative adaptiveness values are calculated as described in
dos Reis et al. (2003, 2004). If s = NULL
, the s values are set to
the optimised values of dos Reis et al. (2004). sking
indicates the
superkingdom, with 0 indicating Eukaryota, and 1 Prokaryota.
Value
A vector of length 60 of relative adaptiveness values.
Author(s)
Mario dos Reis
References
dos Reis M., Wernisch L., and Savva R. (2003) Unexpected correlations between gene expression and codon usage bias from microarray data for the whole Escherichia coli K-12 genome. Nucleic Acids Res., 31: 6976–85.
dos Reis M., Savva R., and Wernisch L. (2004) Solving the riddle of codon usage preferences: a test for translational selection. Nucleic Acids Res., 32: 5036–44.
Examples
eco.ws <- get.ws(tRNA=ecolik12$trna, sking=1)