Split a DNA sequence into codons

This function splits a DNA sequence into a codon sequence.

Usage

base2codon(x, ...)

# S4 method for class 'character'
base2codon(x)

# S4 method for class 'DNAStringSet'
base2codon(x)

# S4 method for class 'DNAMultipleAlignment'
base2codon(x)

Arguments

x

A character string, DNAStringSet-class or DNAMultipleAlignment-class object carrying a DNA sequence.

...

Not in use.

Value

If the argument of 'x' is a character string, then a character vector of codons will be returned. If the argument of 'x' is DNAStringSet-class or DNAMultipleAlignment-class object, then a matrix of codons is returned.

Details

It is expected that the provided DNA sequence is a multiple of 3, otherwise gaps are added to the end of the sequence.

Author

Robersy Sanchez https://genomaths.com. 01/15/2022

Examples

## Gaps are added at the sequence end.
seq <- c("ACCT")
base2codon(x = seq)
#> Warning: *** Base sequence of 'x' is not a multiple of 3. Gaps '-' have been added at the end of the sequence.
#> [1] "ACC" "T--"

## This DNA sequence is a multiple of 3
seq <- c("ACCTCA")
base2codon(x = seq)
#> [1] "ACC" "TCA"

## Load a DNAStringSet. A matrix of codons is returned
data("aln", package = "GenomAutomorphism")
base2codon(x = aln)
#>       [,1]  [,2] 
#>  [1,] "ACC" "ATC"
#>  [2,] "TAT" "TAT"
#>  [3,] "GTT" "GTT"
#>  [4,] "GGT" "GGT"
#>  [5,] "ATT" "ATT"
#>  [6,] "---" "ACG"
#>  [7,] "GCG" "ACG"
#>  [8,] "CTC" "CTC"
#>  [9,] "CAA" "CAA"
#> [10,] "CTC" "TTC"
#> [11,] "CTT" "CTT"
#> [12,] "GGC" "GGG"
#> [13,] "TCT" "TCC"
#> [14,] "AGC" "---"
#> [15,] "TCA" "---"
#> [16,] "CTA" "CTC"
#> [17,] "CAT" "CTT"