get_tai calculates tRNA Adaptation Index (TAI) of each CDS
Arguments
- cf
matrix of codon frequencies as calculated by
count_codons().- trna_w
tRNA weight for each codon, can be generated with
est_trna_weight().
References
dos Reis M, Savva R, Wernisch L. 2004. Solving the riddle of codon usage preferences: a test for translational selection. Nucleic Acids Res 32:5036-5044.
Examples
# calculate TAI of yeast genes based on genomic tRNA copy numbers
w <- est_trna_weight(yeast_trna_gcn)
cf_all <- count_codons(yeast_cds)
tai <- get_tai(cf_all, w)
head(tai)
#> YPL071C YLL050C YMR172W YOR185C YLL032C YBR225W
#> 0.3139989 0.4575092 0.2910314 0.3778311 0.3286790 0.3193323
hist(tai)
