Create a reference codon usage profile from known genes or a set of training sequences.
This profile represents the organism's codon usage bias pattern.
Usage
create_reference_profile(sequences, method = "mean")
Arguments
- sequences
Character vector, DNAStringSet, or list of DNA sequences
- method
Character string: "mean" or "median" for aggregating frequencies
Value
Named numeric vector representing reference codon frequencies
Examples
known_genes <- c("ATGATGATG", "GCCGCCGCC", "TTATTATTA")
ref_profile <- create_reference_profile(known_genes)
