get_fop: Fraction of optimal codons (Fop)

In cubar: Codon Usage Bias Analysis

Fraction of optimal codons (Fop)

Description

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)
hist(fop)

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