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Create custom codon table from amino acid-codon mapping

Source: R/codon_info.R
create_codon_table.Rd

create_codon_table generates a codon table from a user-defined data frame that maps codons to their corresponding amino acids. This function enables analysis of non-standard or artificial genetic codes not available in the NCBI genetic code collection.

Usage

create_codon_table(aa2codon)

Arguments

aa2codon

A data frame with two required columns:

  • amino_acid: Three-letter amino acid abbreviations (e.g., "Ala", "Arg")

  • codon: Corresponding three-nucleotide codon sequences

Value

A data.table with four columns:

  • aa_code: Single-letter amino acid code

  • amino_acid: Three-letter amino acid abbreviation

  • codon: Three-nucleotide codon sequence

  • subfam: Codon subfamily identifier (amino_acid_XY format)

Examples

# View the example amino acid to codon mapping
head(aa2codon)
#>   amino_acid codon
#> 1          *   TAA
#> 2          *   TAG
#> 3          *   TGA
#> 4        Ala   GCT
#> 5        Ala   GCC
#> 6        Ala   GCA

# Create a custom codon table
custom_table <- create_codon_table(aa2codon = aa2codon)
head(custom_table)
#>    aa_code amino_acid  codon subfam
#>     <char>     <char> <char> <char>
#> 1:       *          *    TAA   *_TA
#> 2:       *          *    TAG   *_TA
#> 3:       *          *    TGA   *_TG
#> 4:       A        Ala    GCT Ala_GC
#> 5:       A        Ala    GCC Ala_GC
#> 6:       A        Ala    GCA Ala_GC