cubar (version 1.2.0)

get_gc4d: 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(), level = "subfam")

Value

a named vector of GC4d values. The names of the elements correspond to the sequence names.

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 contents at 4-fold degenerate sites.

Examples

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