get_gc4d {cubar}

GC contents at 4-fold degenerate sites

Description

Calculate GC content at synonymous position of codons (using four-fold degenerate sites only).

Usage

get_gc4d(cf, codon_table = get_codon_table())

Arguments

cf

matrix of codon frequencies as calculated by 'count_codons()'.

codon_table

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

Value

a named vector of GC4d values.

Examples

# estimate GC4d of yeast genes
cf_all <- count_codons(yeast_cds)
gc4d <- get_gc4d(cf_all)
head(gc4d)
hist(gc4d)