get_enc {cubar}

Calculate ENC

Description

get_enc computes ENC of each CDS

Usage

get_enc(cf, codon_table = get_codon_table())

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' or 'create_codon_table'.

Value

vector of ENC values, sequence names are used as vector names

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)
hist(enc)