Calculate TAI — get

get_tai calculates tRNA Adaptation Index (TAI) of each CDS

Usage

get_tai(cf, trna_w, w_format = "cubar")

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().
w_format: tRNA weight values from cubar (default) or the package tAI.

Value

a named vector of TAI values

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 
#> 0.2950724 0.4451196 0.2818316 0.3573874 0.3149884 0.3092542 
hist(tai)