find_synonymous_codons: find_synonymous_codons

In ec363/synonymise: Generate synonymous CDS of frequently used protein motifs, keep DNA synthesis companies happy!

Description

Takes as input a codon and a codon lookup table, find its encoded amino acid, and finds alternative codons for that amino acid and returns them as dataframe (default) or list. Verbose option helps to follow the function as it is working. Is called by synonymise function, but can also be used independently.

Usage

find_synonymous_codons(selectedcodon = NULL, codon_table = codon_table,
  returndf = TRUE, verbose = TRUE)

Arguments

selectedcodon	codon as string, eg "AAA", to be used as the starting codon to find synonyms for.
codon_table	dataframe object to be used as lookup table. Defaults to object named codon_table.
returndf	logical. Should returned object be a dataframe (or if not, then list)? Defaults to TRUE.
verbose	logical. Defaults to TRUE.

Examples

synonymous_codons <- find_synonymous_codons(selectedcodon = "CGC", codon_table = codon_table, returndf = TRUE, verbose = FALSE)

ec363/synonymise documentation built on Aug. 9, 2020, 1:34 a.m.