R: simple numerical encoding of a DNA sequence.

s2n {seqinr} | R Documentation

## simple numerical encoding of a DNA sequence.

### Description

By default, if no `levels` arguments is provided, this function will just code your DNA sequence in integer values following the lexical order `(a > c > g > t)`, that is 0 for "a", 1 for "c", 2 for "g", 3 for "t" and NA for ambiguous bases.

### Usage

    s2n(seq, levels = s2c("acgt"), base4 = TRUE, forceToLower = TRUE)

### Arguments

`seq` | the sequence as a vector of single chars
`levels` | allowed char values, by default a, c, g and t
`base4` | if TRUE the numerical encoding will start at O, if FALSE at 1
`forceToLower` | if TRUE the sequence is forced to lower case caracters

### Value

a vector of integers

### Note

The idea of starting numbering at 0 by default is that it enforces a kind of isomorphism between the paste operator on DNA chars and the + operator on integer coding for DNA chars. By this way, you can work either in the char set, either in the integer set, depending on what is more convenient for your purpose, and then switch from one set to the other one as you like.

### Author(s)

J.R. Lobry

### References

`citation("seqinr")`

### See Also

`n2s`, `factor`, `unclass`

### Examples

    ##
    ## Example of default behaviour:
    ##
    urndna <- s2c("acgt")
    seq <- sample( urndna, 100, replace = TRUE ) ; seq
    s2n(seq)
    ##
    ## How to deal with RNA:
    ##
    urnrna <- s2c("acgt")
    seq <- sample( urnrna, 100, replace = TRUE ) ; seq
    s2n(seq)
    ##
    ## what happens with unknown characters:
    ##
    urnmess <- c(urndna,"n")
    seq <- sample( urnmess, 100, replace = TRUE ) ; seq
    s2n(seq)
    ##
    ## How to change the encoding for unknown characters:
    ##
    tmp <- s2n(seq) ; tmp[is.na(tmp)] <- -1; tmp
    ##
    ## Simple sanity check:
    ##
    stopifnot(all(s2n(s2c("acgt")) == 0:3))

[Package seqinr version 3.4-5 Index]