codon_entropy: Codon entropy

In alexpiper/taxreturn: An R package for retrieving and curating public DNA barcode reference data

Codon entropy

Description

Codon entropy

Usage

codon_entropy(
  x,
  genetic_code = NULL,
  tryrc = TRUE,
  codon_filter = TRUE,
  resolve_draws = "majority",
  method = "ML"
)

Arguments

x	Sequences in DNAStringset or DNAbin format
genetic_code	A genetic code for the Amino acid translation. set to 'SGC4' for Invertebrate mitochondrial or see all known codes at Biostrings::GENETIC_CODE_TABLE
tryrc	Whether the reverse complemement should be evaluated if no frame without stop codons was found in the forward orientation.
codon_filter	Whether taxreturn::codon_filter should be run first to remove sequences containing stop codons or frameshifts.
resolve_draws	How draws should be resolved when multiple possible frames produce sequences with no stop codons. Options are "remove" to completely remove the sequence, or "majority" to pick the most common frame from the entire alignment.
method	the method employed to estimate entropy. see ?entropy::entropy for more details

alexpiper/taxreturn documentation built on Sept. 14, 2024, 7:56 p.m.