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GC contents at synonymous 3rd codon positions

Source: R/gene_index.R
get_gc3s.Rd

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)
#>   YPL071C   YLL050C   YMR172W   YOR185C   YLL032C   YBR225W 
#> 0.3082192 0.3571429 0.3902439 0.3474178 0.3204489 0.3375143 
hist(gc3s)