count_codons {cubar}

Count occurrences of different codons

Description

count_codons tabulates the occurrences of all the 64 codons in input CDSs

Usage

count_codons(seqs, ...)

Arguments

seqs

CDS sequences, DNAStringSet.

...

additional arguments passed to 'Biostrings::trinucleotideFrequency'.

Value

matrix of codon (column) frequencies of each CDS (row).

Examples

# count codon occurrences
cf_all <- count_codons(yeast_cds)
dim(cf_all)
cf_all[1:5, 1:5]
count_codons(yeast_cds[1])