Fraction of optimal codons (Fop) — get

get_fop calculates the fraction of optimal codons (Fop) of each CDS.

Usage

get_fop(cf, op = NULL, codon_table = get_codon_table(), ...)

Arguments

cf: matrix of codon frequencies as calculated by count_codons().
op: a character vector of optimal codons. Can be determined automatically by running est_optimal_codons.
codon_table: a table of genetic code derived from get_codon_table or create_codon_table.
...: other arguments passed to est_optimal_codons.

Value

a named vector of fop values.

References

Ikemura T. 1981. Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system. J Mol Biol 151:389-409.

Examples

# estimate Fop of yeast genes
cf_all <- count_codons(yeast_cds)
fop <- get_fop(cf_all)
head(fop)
#>   YPL071C   YLL050C   YMR172W   YOR185C   YLL032C   YBR225W 
#> 0.4012739 0.7569444 0.4611111 0.5791855 0.4963680 0.4716981 
hist(fop)