get_tai {cubar}

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)