get_tai: Calculate TAI

In cubar: Codon Usage Bias Analysis

Calculate TAI

Description

get_tai calculates tRNA Adaptation Index (TAI) of each CDS

Usage

get_tai(cf, trna_w)

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().

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)
hist(tai)

cubar documentation built on April 3, 2025, 8:58 p.m.