est_optimal_codons {cubar}

Estimate optimal codons

Description

est_toptimal_codons determine optimal codon of each codon family with binomial regression. Usage of optimal codons should correlate negatively with enc.

Usage

est_optimal_codons(seqs, codon_table = get_codon_table())

Arguments

seqs

CDS sequences of all protein-coding genes. One for each gene.

codon_table

a table of genetic code derived from 'get_codon_table' or 'create_codon_table'.

Value

data.table of optimal codons

Examples

# perform binomial regression for optimal codon estimation
codons_opt <- est_optimal_codons(yeast_cds)
# select optimal codons with a fdr of 0.001
codons_opt <- codons_opt[qvalue < 0.001 & coef < 0]
codons_opt