get_enc
computes ENC of each CDS
Usage
get_enc(cf, codon_table = get_codon_table(), level = "subfam")
Arguments
- cf
matrix of codon frequencies as calculated by
count_codons()
.- codon_table
codon_table a table of genetic code derived from
get_codon_table
orcreate_codon_table
.- level
"subfam" (default) or "amino_acid". For which level to determine ENC.
References
- Wright F. 1990. The 'effective number of codons' used in a gene. Gene 87:23-29. - Sun X, Yang Q, Xia X. 2013. An improved implementation of effective number of codons (NC). Mol Biol Evol 30:191-196.
Examples
# estimate ENC of yeast genes
cf_all <- count_codons(yeast_cds)
enc <- get_enc(cf_all)
head(enc)
#> YPL071C YLL050C YMR172W YOR185C YLL032C YBR225W
#> 52.93616 44.57694 56.03833 50.82037 53.34254 53.85807
hist(enc)