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. The names of the elements correspond to the sequence names.

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 
#> 0.4315068 0.7785714 0.4763271 0.6009390 0.5112219 0.4846066 
hist(fop)