get_gc3s: GC contents at synonymous 3rd codon positions

In cubar: Codon Usage Bias Analysis

GC contents at synonymous 3rd codon positions

Description

Calculate GC content at synonymous 3rd codon positions.

Usage

get_gc3s(cf, codon_table = get_codon_table(), level = "subfam")

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.
level	"subfam" (default) or "amino_acid". For which level to determine GC content at synonymous 3rd codon positions.

Value

a named vector of GC3s values.

References

Peden JF. 2000. Analysis of codon usage.

Examples

# estimate GC3s of yeast genes
cf_all <- count_codons(yeast_cds)
gc3s <- get_gc3s(cf_all)
head(gc3s)
hist(gc3s)

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